diff --git a/src/BondAdjacencyList.cpp b/src/BondAdjacencyList.cpp index 0569174cd..d14d8037b 100644 --- a/src/BondAdjacencyList.cpp +++ b/src/BondAdjacencyList.cpp @@ -22,7 +22,7 @@ adjNode* BondAdjacencyList::getAdjListNode(int value, int weight, adjNode* head) return newNode; } -BondAdjacencyList::BondAdjacencyList(FILE* psf, uint nAtoms, uint nBonds, std::vector< std::vector > & moleculeXAtomIDY){ +BondAdjacencyList::BondAdjacencyList(FILE* psf, uint nAtoms, uint nBonds, std::vector< std::vector > & moleculeXAtomIDY){ this->nAtoms = nAtoms; this->nBonds = nBonds; @@ -75,18 +75,19 @@ BondAdjacencyList::BondAdjacencyList(FILE* psf, uint nAtoms, uint nBonds, std::v connectedComponents(moleculeXAtomIDY); /* Sort Atom Indices in N connected components, then sort N connected components by first atom index*/ - for (std::vector< std::vector >::iterator it = moleculeXAtomIDY.begin(); + for (std::vector< std::vector >::iterator it = moleculeXAtomIDY.begin(); it != moleculeXAtomIDY.end(); it++){ std::sort(it->begin(), it->end()); } std::sort(moleculeXAtomIDY.begin(), moleculeXAtomIDY.end()); +/* #ifndef NDEBUG std::cout << "Adjacency List" << std::endl; for (uint i = 0; i < nAtoms; i++) display_AdjList(head[i], i); std::cout << "Connected Components" << std::endl; - for (std::vector< std::vector >::iterator it = moleculeXAtomIDY.begin(); + for (std::vector< std::vector >::iterator it = moleculeXAtomIDY.begin(); it != moleculeXAtomIDY.end(); it++){ for (std::vector::iterator it2 = it->begin(); it2 != it->end(); it2++){ @@ -95,7 +96,7 @@ BondAdjacencyList::BondAdjacencyList(FILE* psf, uint nAtoms, uint nBonds, std::v std::cout << std::endl; } #endif - +*/ } // Destructor @@ -124,7 +125,7 @@ void BondAdjacencyList::display_AdjList(adjNode* ptr, int i) // Method to print connected components in an // undirected graph -void BondAdjacencyList::connectedComponents(std::vector< std::vector > & moleculeXAtomIDY) +void BondAdjacencyList::connectedComponents(std::vector< std::vector > & moleculeXAtomIDY) { // Mark all the vertices as not visited bool *visited = new bool[nAtoms]; @@ -139,7 +140,7 @@ void BondAdjacencyList::connectedComponents(std::vector< std::vector > & m // from v /* For debugging std::cout << "Calling DFSUtil" << std::endl; */ - std::vector moleculeX; + std::vector moleculeX; DFSUtil(v, this->head[v], this->head, visited, moleculeX); moleculeXAtomIDY.push_back(moleculeX); /* For debugging std::cout << "\n"; */ @@ -148,7 +149,7 @@ void BondAdjacencyList::connectedComponents(std::vector< std::vector > & m delete[] visited; } -void BondAdjacencyList::DFSUtil(int v, adjNode * node, adjNode ** head, bool * visited, std::vector & moleculeX) +void BondAdjacencyList::DFSUtil(int v, adjNode * node, adjNode ** head, bool * visited, std::vector & moleculeX) { // Mark the current node as visited and print it visited[v] = true; diff --git a/src/BondAdjacencyList.h b/src/BondAdjacencyList.h index 4b1d2f690..f5274ba71 100644 --- a/src/BondAdjacencyList.h +++ b/src/BondAdjacencyList.h @@ -37,12 +37,12 @@ uint nAtoms; // number of nodes in the graph uint nBonds; // number of edges in the graph -BondAdjacencyList(FILE* psf, uint nAtoms, uint nBonds, std::vector< std::vector > & moleculeXAtomIDY); +BondAdjacencyList(FILE* psf, uint nAtoms, uint nBonds, std::vector< std::vector > & moleculeXAtomIDY); ~BondAdjacencyList(); adjNode* getAdjListNode(int value, int weight, adjNode* head); void display_AdjList(adjNode* ptr, int i); -void connectedComponents(std::vector< std::vector > & moleculeXAtomIDY); -void DFSUtil(int v, adjNode * node, adjNode ** head, bool * visited, std::vector & moleculeX); +void connectedComponents(std::vector< std::vector > & moleculeXAtomIDY); +void DFSUtil(int v, adjNode * node, adjNode ** head, bool * visited, std::vector & moleculeX); graphEdge * edges; diff --git a/src/MolSetup.cpp b/src/MolSetup.cpp index e2680441d..169d8805c 100644 --- a/src/MolSetup.cpp +++ b/src/MolSetup.cpp @@ -47,6 +47,7 @@ namespace { //Assigns numerical mol kind indices to all molKinds void AssignMolKinds(MolKind& kind, const pdb_setup::Atoms& pdbData, const std::string& name); +void AssignMolKinds(MolKind& kind, const mol_setup::MoleculeVariables& molVars, const std::string& name); void AssignAtomKinds(MolKind& kind, const FFSetup& ffData); void AssignBondKinds(MolKind& kind, const FFSetup& ffData); void AssignAngleKinds(MolKind& kind, const FFSetup& ffData); @@ -59,7 +60,7 @@ void BriefDihKinds(MolKind& kind, const FFSetup& ffData); //Builds kindMap from PSF file (does not include coordinates) kindMap // should be empty returns number of atoms in the file, or errors::READ_ERROR if // the read failed somehow -int ReadPSF(const char* psfFilename, MolMap& kindMap, SizeMap& sizeMap, pdb_setup::Atoms& pdbData, MolMap * kindMapFromBox1 = NULL, SizeMap * sizeMapFromBox1 = NULL); +int ReadPSF(const char* psfFilename, MoleculeVariables & molVars, MolMap& kindMap, SizeMap& sizeMap, pdb_setup::Atoms& pdbData, MolMap * kindMapFromBox1 = NULL, SizeMap * sizeMapFromBox1 = NULL); //adds atoms and molecule data in psf to kindMap //pre: stream is at !NATOMS post: stream is at end of atom section int ReadPSFAtoms(FILE* psf, @@ -210,13 +211,14 @@ std::vector mol_setup::BondsAll(const MolKind& molKind) return result; } -int mol_setup::ReadCombinePSF(MolMap& kindMap, +int mol_setup::ReadCombinePSF(MoleculeVariables & molVars, + MolMap& kindMap, SizeMap& sizeMap, std::string const*const psfFilename, const bool* psfDefined, pdb_setup::Atoms& pdbAtoms) { - int errorcode = ReadPSF(psfFilename[0].c_str(), kindMap, sizeMap, pdbAtoms); + int errorcode = ReadPSF(psfFilename[0].c_str(), molVars, kindMap, sizeMap, pdbAtoms); int nAtoms = errorcode; if (errorcode < 0) return errorcode; @@ -224,7 +226,7 @@ int mol_setup::ReadCombinePSF(MolMap& kindMap, SizeMap sizeMap2; if (pdbAtoms.count != nAtoms && BOX_TOTAL == 2 && psfDefined[1]) { map2.clear(); - errorcode = ReadPSF(psfFilename[1].c_str(), map2, sizeMap2, pdbAtoms, &kindMap, &sizeMap); + errorcode = ReadPSF(psfFilename[1].c_str(), molVars, map2, sizeMap2, pdbAtoms, &kindMap, &sizeMap); nAtoms += errorcode; if (errorcode < 0) return errorcode; @@ -249,15 +251,15 @@ int MolSetup::Init(const config_setup::RestartSettings& restart, { kindMap.clear(); sizeMap.clear(); - return ReadCombinePSF(kindMap, sizeMap, psfFilename, psfDefined, pdbAtoms); + return ReadCombinePSF(molVars, kindMap, sizeMap, psfFilename, psfDefined, pdbAtoms); } -void MolSetup::AssignKinds(const pdb_setup::Atoms& pdbAtoms, const FFSetup& ffData) +void MolSetup::AssignKinds(const mol_setup::MoleculeVariables& molVars, const FFSetup& ffData) { typedef MolMap::iterator MapIt; for (MapIt it = kindMap.begin(), end = kindMap.end(); it != end; ++it) { - AssignMolKinds(it->second, pdbAtoms, it->first); + AssignMolKinds(it->second, molVars, it->first); AssignAtomKinds(it->second, ffData); AssignBondKinds(it->second, ffData); AssignAngleKinds(it->second, ffData); @@ -312,38 +314,97 @@ int read_atoms(FILE *psf, unsigned int nAtoms, std::vector & al return 0; } -typedef std::vector::const_iterator candidateIterator; +typedef std::vector::const_iterator candidateIterator; -void createMapAndModifyPDBAtomDataStructure(const BondAdjacencyList & bondAdjList, - const std::vector< std::vector > & moleculeXAtomIDY, - std::vector & allAtoms, - mol_setup::MolMap & kindMap, - mol_setup::SizeMap & sizeMap, - pdb_setup::Atoms& pdbAtoms, - mol_setup::MolMap * kindMapFromBox1, - mol_setup::SizeMap * sizeMapFromBox1){ +void createKindMap (pdb_setup::Atoms& pdbAtoms, + mol_setup::MoleculeVariables & molVars, + const BondAdjacencyList & bondAdjList, + std::vector< std::vector > & moleculeXAtomIDY, + std::vector & allAtoms, + mol_setup::MolMap & kindMap, + mol_setup::SizeMap & sizeMap, + mol_setup::MolMap * kindMapFromBox1, + mol_setup::SizeMap * sizeMapFromBox1){ /* A size -> moleculeKind map for quick evaluation of new molecules based on molMap entries of a given size exisitng or not */ uint startIdxResBoxOffset; uint resKindIndex; - if (pdbAtoms.lastAtomIndexInBox0 == 0){ + if (molVars.lastAtomIndexInBox0 == 0){ startIdxResBoxOffset = 0; resKindIndex = 0; - pdbAtoms.startIdxRes.clear(); - pdbAtoms.resKinds.clear(); - pdbAtoms.resKindNames.clear(); - pdbAtoms.resNames.clear(); + + molVars.startIdxMolecules.clear(); + molVars.moleculeKinds.clear(); + molVars.moleculeKindNames.clear(); + molVars.moleculeNames.clear(); + } else { - startIdxResBoxOffset = pdbAtoms.lastAtomIndexInBox0 + 1; - resKindIndex = pdbAtoms.lastResKindIndex; + startIdxResBoxOffset = molVars.lastAtomIndexInBox0 + 1; + resKindIndex = molVars.lastResKindIndex; } + uint residueIDTemp; + uint pdbDataResidueSize; + uint firstAtomOfPorousIndex; + bool firstAtomOfPorous = true; + /* Before we begin, we must consolidate porous materials into one molecule. + Our way of detecting porous molecules are nonbonded atoms which have the same residue id. + Alternatively, one may think about it as the opposite of the protein problem where the + molecule was larger than a single residue. Here the molecule is smaller than the residue, + since we define the molecule as a connected component. + + To solve: + We will append the atom id's onto the vector entry in moleculeXAtomIDY of the first atom + in the residue until the size of the molecule matches the residue length. We assign -1 + to all the atoms we append, and we skip over these negative indices in the parsing process. + + We assume that the number of atoms of a connected component is greater than or equal to + the number of atoms in the first residue of the molecule, otherwise it is a porous material. + + We do support porous materials made up of connected components.size() > 1, + i.e. a wall of waters all with the same residue id. + + */ + for ( int i = 0; i < moleculeXAtomIDY.size(); i++){ + /* Residue's are numbered starting from 1 */ + residueIDTemp = allAtoms[moleculeXAtomIDY[i].front()].residueID - 1; + /* startIdxRes is short for startIdxResidue */ + // pdbAtoms.startIdxRes[residueIDTemp + 1] is array oob + if (pdbAtoms.startIdxRes.size() == residueIDTemp + 1) { + pdbDataResidueSize = pdbAtoms.x.size() - pdbAtoms.startIdxRes[residueIDTemp]; + } else { + pdbDataResidueSize = pdbAtoms.startIdxRes[residueIDTemp + 1] - pdbAtoms.startIdxRes[residueIDTemp]; + } + /* We assume that the number of atoms of a connected component is greater than or equal to + the number of atoms in the first residue of the molecule, otherwise it is a porous material. + */ + if (pdbDataResidueSize > moleculeXAtomIDY[i].size()){ + if(firstAtomOfPorous){ + firstAtomOfPorousIndex = i; + firstAtomOfPorous = false; + } else { + for (std::vector::const_iterator connectedComponentIt = moleculeXAtomIDY[i].cbegin(); + connectedComponentIt != moleculeXAtomIDY[i].cend(); connectedComponentIt++){ + moleculeXAtomIDY[firstAtomOfPorousIndex].push_back(*connectedComponentIt); + } + moleculeXAtomIDY[i].front() = -1; + /* We have constructed a molecule out of the disjoint atoms of the porous material */ + if(moleculeXAtomIDY[firstAtomOfPorousIndex].size() == pdbDataResidueSize){ + firstAtomOfPorous = true; + } + } + } + } /* Iterate through N connected components */ int stringSuffix = 1; - for (std::vector< std::vector >::const_iterator it = moleculeXAtomIDY.cbegin(); + for (std::vector< std::vector >::const_iterator it = moleculeXAtomIDY.cbegin(); it != moleculeXAtomIDY.cend(); it++){ + + /* Only way to have this value is a porous material which was consoldated above */ + if (it->front() == -1) + continue; std::string fragName; bool multiResidue = false; @@ -378,10 +439,12 @@ void createMapAndModifyPDBAtomDataStructure(const BondAdjacencyList & bondAdjLis /* Get the map key */ fragName = *sizeConsistentEntries; - /* Boilerplate PDB Data modifications for matches */ - pdbAtoms.startIdxRes.push_back(startIdxResBoxOffset + it->front()); - pdbAtoms.resKinds.push_back((*kindMapFromBox1)[fragName].kindIndex); - pdbAtoms.resNames.push_back(fragName); + /* Boilerplate Molecule Index/Name vector entries for matches */ + + molVars.startIdxMolecules.push_back(startIdxResBoxOffset + it->front()); + molVars.moleculeKinds.push_back((*kindMapFromBox1)[fragName].kindIndex); + molVars.moleculeNames.push_back(fragName); + newMapEntry = false; /* Boilerplate PDB Data modifications for matches */ @@ -398,7 +461,7 @@ void createMapAndModifyPDBAtomDataStructure(const BondAdjacencyList & bondAdjLis if((*kindMapFromBox1)[fragName].isMultiResidue){ kindMap[fragName] = MolKind(); kindMap[fragName].isMultiResidue = true; - for (std::vector::const_iterator connectedComponentIt = it->cbegin(); + for (std::vector::const_iterator connectedComponentIt = it->cbegin(); connectedComponentIt != it->cend(); connectedComponentIt++){ kindMap[fragName].atoms.push_back(allAtoms[*connectedComponentIt]); kindMap[fragName].intraMoleculeResIDs.push_back(allAtoms[*connectedComponentIt].residueID); @@ -411,7 +474,7 @@ void createMapAndModifyPDBAtomDataStructure(const BondAdjacencyList & bondAdjLis } else { kindMap[fragName] = MolKind(); kindMap[fragName].isMultiResidue = false; - for (std::vector::const_iterator connectedComponentIt = it->cbegin(); + for (std::vector::const_iterator connectedComponentIt = it->cbegin(); connectedComponentIt != it->cend(); connectedComponentIt++){ kindMap[fragName].atoms.push_back(allAtoms[*connectedComponentIt]); } @@ -455,7 +518,7 @@ void createMapAndModifyPDBAtomDataStructure(const BondAdjacencyList & bondAdjLis bool newSize = false; bool newMapEntry = true; - typedef std::vector::const_iterator candidateIterator; + typedef std::vector::const_iterator candidateIterator; /* Found no matching molecules by size */ if (sizeIt == sizeMap.end()) { newSize = true; @@ -476,10 +539,11 @@ void createMapAndModifyPDBAtomDataStructure(const BondAdjacencyList & bondAdjLis } // Found a match if (itPair.second == it->cend()) { - // Modify PDBData - pdbAtoms.startIdxRes.push_back(startIdxResBoxOffset + it->front()); - pdbAtoms.resKinds.push_back(kindMap[*sizeConsistentEntries].kindIndex); - pdbAtoms.resNames.push_back(*sizeConsistentEntries); + + molVars.startIdxMolecules.push_back(startIdxResBoxOffset + it->front()); + molVars.moleculeKinds.push_back(kindMap[*sizeConsistentEntries].kindIndex); + molVars.moleculeNames.push_back(*sizeConsistentEntries); + newMapEntry = false; break; } @@ -516,7 +580,7 @@ void createMapAndModifyPDBAtomDataStructure(const BondAdjacencyList & bondAdjLis kindMap[fragName] = MolKind(); kindMap[fragName].isMultiResidue = true; - for (std::vector::const_iterator connectedComponentIt = it->cbegin(); + for (std::vector::const_iterator connectedComponentIt = it->cbegin(); connectedComponentIt != it->cend(); connectedComponentIt++){ kindMap[fragName].atoms.push_back(allAtoms[*connectedComponentIt]); kindMap[fragName].intraMoleculeResIDs.push_back(allAtoms[*connectedComponentIt].residueID); @@ -530,7 +594,7 @@ void createMapAndModifyPDBAtomDataStructure(const BondAdjacencyList & bondAdjLis fragName = allAtoms[it->front()].residue; kindMap[allAtoms[it->front()].residue] = MolKind(); kindMap[fragName].isMultiResidue = false; - for (std::vector::const_iterator connectedComponentIt = it->cbegin(); + for (std::vector::const_iterator connectedComponentIt = it->cbegin(); connectedComponentIt != it->cend(); connectedComponentIt++){ kindMap[fragName].atoms.push_back(allAtoms[*connectedComponentIt]); } @@ -538,11 +602,12 @@ void createMapAndModifyPDBAtomDataStructure(const BondAdjacencyList & bondAdjLis kindMap[fragName].firstAtomID = it->front() + 1; kindMap[fragName].firstMolID = allAtoms[it->front()].residueID; kindMap[fragName].kindIndex = resKindIndex; - //pdbAtoms.startIdxRes.push_back(kindMap[fragName].firstAtomID - 1); - pdbAtoms.startIdxRes.push_back(startIdxResBoxOffset + kindMap[fragName].firstAtomID - 1); - pdbAtoms.resKinds.push_back(kindMap[fragName].kindIndex); - pdbAtoms.resKindNames.push_back(fragName); - pdbAtoms.resNames.push_back(fragName); + + molVars.startIdxMolecules.push_back(startIdxResBoxOffset + kindMap[fragName].firstAtomID - 1); + molVars.moleculeKinds.push_back(kindMap[fragName].kindIndex); + molVars.moleculeKindNames.push_back(fragName); + molVars.moleculeNames.push_back(fragName); + MolSetup::copyBondInfoIntoMapEntry(bondAdjList, kindMap, fragName); resKindIndex++; if (newSize){ @@ -553,8 +618,8 @@ void createMapAndModifyPDBAtomDataStructure(const BondAdjacencyList & bondAdjLis } } } - pdbAtoms.lastAtomIndexInBox0 = (moleculeXAtomIDY.back()).back(); - pdbAtoms.lastResKindIndex = resKindIndex; + molVars.lastAtomIndexInBox0 = (moleculeXAtomIDY.back()).back(); + molVars.lastResKindIndex = resKindIndex; } typedef std::map MolMap; @@ -578,13 +643,21 @@ void MolSetup::copyBondInfoIntoMapEntry(const BondAdjacencyList & bondAdjList, m namespace { -void AssignMolKinds(MolKind& kind, const pdb_setup::Atoms& pdbData, const std::string& name) +/* Currently unused, would be useful for number of aa's in a protein */ +void AssignResKinds(MolKind& kind, const pdb_setup::Atoms& pdbData, const std::string& name) { uint index = std::find(pdbData.resKindNames.begin(), pdbData.resKindNames.end(), name) - pdbData.resKindNames.begin(); kind.kindIndex = index; } +void AssignMolKinds(MolKind& kind, const mol_setup::MoleculeVariables& molVars, const std::string& name) +{ + uint index = std::find(molVars.moleculeKindNames.begin(), + molVars.moleculeKindNames.end(), name) - molVars.moleculeKindNames.begin(); + kind.kindIndex = index; +} + void AssignAtomKinds(MolKind& kind, const FFSetup& ffData) { for (uint i = 0; i < kind.atoms.size(); ++i) { @@ -839,7 +912,7 @@ namespace { //Initializes system from PSF file (does not include coordinates) //returns number of atoms in the file, or errors::READ_ERROR if the read failed somehow -int ReadPSF(const char* psfFilename, MolMap& kindMap, SizeMap & sizeMap, pdb_setup::Atoms& pdbData, MolMap * kindMapFromBox1, SizeMap * sizeMapFromBox1) +int ReadPSF(const char* psfFilename, MoleculeVariables & molVars, MolMap& kindMap, SizeMap & sizeMap, pdb_setup::Atoms& pdbData, MolMap * kindMapFromBox1, SizeMap * sizeMapFromBox1) { FILE* psf = fopen(psfFilename, "r"); char* check; //return value of fgets @@ -897,7 +970,7 @@ int ReadPSF(const char* psfFilename, MolMap& kindMap, SizeMap & sizeMap, pdb_set . X - molecule M */ - std::vector< std::vector > moleculeXAtomIDY; + std::vector< std::vector > moleculeXAtomIDY; /* A standard adjacency list with N nodes, where N is number of atoms. This is an undirected graph, where edges between nodes represent bonds between atoms. It is generated by DFS, checking if a node @@ -920,17 +993,19 @@ int ReadPSF(const char* psfFilename, MolMap& kindMap, SizeMap & sizeMap, pdb_set The bond information contained in the Adjacency list is assigned to map entries. - Finally, entries in startIDxRes are consolidated redefine the start and end of molecule, - as far as the pdb data is concerned. + Finally, entries in startIDxRes are used for checking if a molecule is smaller than the residue, + which is the case for porous materials, which are a series of non-bonded (by current MosDef implementation) + yet associated molecules. */ - createMapAndModifyPDBAtomDataStructure( bondAdjList, - moleculeXAtomIDY, - allAtoms, - kindMap, - sizeMap, - pdbData, - kindMapFromBox1, - sizeMapFromBox1); + createKindMap(pdbData, + molVars, + bondAdjList, + moleculeXAtomIDY, + allAtoms, + kindMap, + sizeMap, + kindMapFromBox1, + sizeMapFromBox1); std::vector > firstAtomLookup; for (MolMap::iterator it = kindMap.begin(); it != kindMap.end(); ++it) { diff --git a/src/MolSetup.h b/src/MolSetup.h index dde9ca31f..8985b6cc7 100644 --- a/src/MolSetup.h +++ b/src/MolSetup.h @@ -27,6 +27,14 @@ class FFSetup; namespace mol_setup { + +struct MoleculeVariables { + std::vector startIdxMolecules, moleculeKinds; + std::vector moleculeNames, moleculeKindNames; + uint lastAtomIndexInBox0 = 0; + uint lastResKindIndex = 0; +}; + //!structure to contain an atom's data during initialization class Atom { @@ -146,7 +154,7 @@ typedef std::map > SizeMap; *\param numFiles number of files to read *\return -1 if failed, 0 if successful */ -int ReadCombinePSF(MolMap& kindMap, SizeMap& sizeMap, const std::string* psfFilename, +int ReadCombinePSF(MoleculeVariables & molVars, MolMap& kindMap, SizeMap& sizeMap, const std::string* psfFilename, const bool* psfDefined, pdb_setup::Atoms& pdbAtoms); void PrintMolMapVerbose(const MolMap& kindMap); @@ -159,14 +167,15 @@ class MolSetup public: class Atom; int read_atoms(FILE *, unsigned int nAtoms, std::vector & allAtoms); - void createMapAndModifyPDBAtomDataStructure(const BondAdjacencyList & bondAdjList, - const std::vector< std::vector > & moleculeXAtomIDY, - std::vector & allAtoms, - mol_setup::MolMap & kindMap, - mol_setup::SizeMap & sizeMap, - pdb_setup::Atoms& pdbAtoms, - mol_setup::MolMap * kindMapFromBox1, - mol_setup::SizeMap * sizeMapFromBox1); + void createKindMap (pdb_setup::Atoms& pdbAtoms, + mol_setup::MoleculeVariables & molVars, + const BondAdjacencyList & bondAdjList, + std::vector< std::vector > & moleculeXAtomIDY, + std::vector & allAtoms, + mol_setup::MolMap & kindMap, + mol_setup::SizeMap & sizeMap, + mol_setup::MolMap * kindMapFromBox1, + mol_setup::SizeMap * sizeMapFromBox1); static void copyBondInfoIntoMapEntry(const BondAdjacencyList & bondAdjList, mol_setup::MolMap & kindMap, std::string fragName); @@ -178,10 +187,11 @@ class MolSetup const bool* psfDefined, pdb_setup::Atoms& pdbAtoms); - void AssignKinds(const pdb_setup::Atoms& pdbAtoms, const FFSetup& ffData); + void AssignKinds(const mol_setup::MoleculeVariables& molVars, const FFSetup& ffData); //private: mol_setup::MolMap kindMap; mol_setup::SizeMap sizeMap; + mol_setup::MoleculeVariables molVars; }; #endif diff --git a/src/Molecules.cpp b/src/Molecules.cpp index 91cecac4b..06e29f3ed 100644 --- a/src/Molecules.cpp +++ b/src/Molecules.cpp @@ -43,23 +43,25 @@ void Molecules::Init(Setup & setup, Forcefield & forcefield, kinds = new MoleculeKind[kindsCount]; //Molecule instance arrays/data - count = atoms.startIdxRes.size(); + count = setup.mol.molVars.startIdxMolecules.size(); if (count == 0) { std::cerr << "Error: No Molecule was found in the PDB file(s)!" << std::endl; exit(EXIT_FAILURE); } start = new uint [count + 1]; - start = vect::TransferInto(start, atoms.startIdxRes); + start = vect::TransferInto(start, setup.mol.molVars.startIdxMolecules); start[count] = atoms.x.size(); - kIndex = vect::transfer(atoms.resKinds); - kIndexCount = atoms.resKinds.size(); + + kIndex = vect::transfer(setup.mol.molVars.moleculeKinds); + kIndexCount = setup.mol.molVars.moleculeKinds.size(); + chain = vect::transfer(atoms.chainLetter); for (uint mk = 0 ; mk < kindsCount; mk++) { countByKind[mk] = - std::count(atoms.resNames.begin(), atoms.resNames.end(), - atoms.resKindNames[mk]); - kinds[mk].Init(atoms.resKindNames[mk], setup, forcefield, sys); + std::count(setup.mol.molVars.moleculeNames.begin(), setup.mol.molVars.moleculeNames.end(), + setup.mol.molVars.moleculeKindNames[mk]); + kinds[mk].Init(setup.mol.molVars.moleculeKindNames[mk], setup, forcefield, sys); } #if ENSEMBLE == GCMC diff --git a/src/PDBSetup.h b/src/PDBSetup.h index c607aa307..b5c08e11e 100644 --- a/src/PDBSetup.h +++ b/src/PDBSetup.h @@ -132,8 +132,6 @@ class Atoms : public FWReadableBase uint numAtomsInBox[BOX_TOTAL]; // number of atom in each box std::string currResname; - uint lastAtomIndexInBox0 = 0; - uint lastResKindIndex = 0; }; } diff --git a/src/PSFOutput.cpp b/src/PSFOutput.cpp index 22e03d730..37c20db21 100644 --- a/src/PSFOutput.cpp +++ b/src/PSFOutput.cpp @@ -37,12 +37,12 @@ const int dihPerLine = 2; PSFOutput::PSFOutput(const Molecules& molecules, const System &sys, Setup & set) : - molecules(&molecules), molNames(set.pdb.atoms.resKindNames), + molecules(&molecules), molNames(set.mol.molVars.moleculeKindNames), molLookRef(sys.molLookup) { molKinds.resize(set.mol.kindMap.size()); - for(uint i = 0; i < set.pdb.atoms.resKindNames.size(); ++i) { - molKinds[i] = set.mol.kindMap[set.pdb.atoms.resKindNames[i]]; + for(uint i = 0; i < set.mol.molVars.moleculeKindNames.size(); ++i) { + molKinds[i] = set.mol.kindMap[set.mol.molVars.moleculeKindNames[i]]; } CountMolecules(); PrintPSF(set.config.out.state.files.psf.name); diff --git a/src/Setup.h b/src/Setup.h index eadc0084c..3b2778ea6 100644 --- a/src/Setup.h +++ b/src/Setup.h @@ -55,7 +55,7 @@ class Setup if(mol.Init(config.in.restart, config.in.files.psf.name, config.in.files.psf.defined, pdb.atoms) != 0) { exit(EXIT_FAILURE); } - mol.AssignKinds(pdb.atoms, ff); + mol.AssignKinds(mol.molVars, ff); } }; diff --git a/test/FileList.cmake b/test/FileList.cmake index 5f2f41af8..8770b009f 100644 --- a/test/FileList.cmake +++ b/test/FileList.cmake @@ -1,5 +1,6 @@ set(TestSources test/src/BasicTypesTest.cpp test/src/BitLibTest.cpp + test/src/PSFParserTest.cpp test/src/EndianTest.cpp ) \ No newline at end of file diff --git a/test/GoogleTest.cmake b/test/GoogleTest.cmake index 6ac3e23ae..b0e65841a 100644 --- a/test/GoogleTest.cmake +++ b/test/GoogleTest.cmake @@ -36,4 +36,5 @@ include(test/FileList.cmake) # Now simply link against gtest or gtest_main as needed. Eg add_executable(GOMC_Test ${TestSources}) target_link_libraries(GOMC_Test gtest_main) -add_test(NAME BasicTypesTest COMMAND BasicTypesTest) \ No newline at end of file +add_test(NAME BasicTypesTest COMMAND BasicTypesTest) +add_test(NAME PSFParserTest COMMAND PSFParserTest) \ No newline at end of file diff --git a/test/input/GOMC_GEMC.conf b/test/input/GOMC_GEMC.conf new file mode 100644 index 000000000..7e9f04f43 --- /dev/null +++ b/test/input/GOMC_GEMC.conf @@ -0,0 +1,157 @@ +######################## +#Control file for SPCE water at 350K +######################## + +############################################################################ +# ========-------------------- INPUT --------------------------=========== +############################################################################ + +######################### +# enable, step +######################### +Restart false + + +#################################### +# kind {RESTART, RANDOM, INTSEED} +#################################### +PRNG RANDOM + +#################################### +# FORCE FIELD +#################################### +ParaTypeCHARMM true + +Parameters ./water.par +Parameters ./GOMC_water_FF.inp +#################################### +# INPUT PDB FILES +#################################### +Coordinates 0 ./PSFParser/BOX_0.pdb +Coordinates 1 ./PSFParser/BOX_1.pdb + +#################################### +# INPUT PSF FILES +#################################### +Structure 0 ./PSFParser/BOX_0.psf +Structure 1 ./PSFParser/BOX_1.psf + +############################################################################ +# =======--------------------- SYSTEM --------------------------=========== +############################################################################ +################################## +# GEMC TYPE (DEFULT IS NVT_GEMC) +################################## +GEMC NVT + +############################# +# SIMULATION CONDITION +############################# +Temperature 350 +Potential SWITCH +Rswitch 10.0 +LRC true +Rcut 12 +RcutLow 0.1 # was set to 1.2 +Exclude 1-4 + +############################# +# ELECTROSTATIC +############################# +Ewald true +ElectroStatic true +CachedFourier false +Tolerance 0.00001 +1-4scaling false + + +############################### +# PRESSURE CALCULATION +################################ +PressureCalc true 5000 + +################################ +# STEPS +################################ +RunSteps 10 +EqSteps 5 +AdjSteps 2 + + + +################################ +# MOVE FREQUENCY +################################ + +VolFreq 0.01 +MultiParticleFreq 0.01 +DisFreq 0.18 +RotFreq 0.10 +RegrowthFreq 0.10 +#IntraMEMC-2Freq 0.10 +IntraSwapFreq 0.10 +#MEMC-2Freq 0.25 +SwapFreq 0.50 + +################################ +# BOX DIMENSION #, X, Y, Z +################################ +CellBasisVector1 0 40.0 0.00 0.00 +CellBasisVector2 0 0.00 40.0 0.00 +CellBasisVector3 0 0.00 0.00 40.0 + +CellBasisVector1 1 200.00 0.00 0.00 +CellBasisVector2 1 0.00 200.00 0.00 +CellBasisVector3 1 0.00 0.00 200.00 + + + +############################## +# CBMC TRIALS +############################## +CBMC_First 16 +CBMC_Nth 8 +CBMC_Ang 50 +CBMC_Dih 50 + + +############################################################################ +# =======-------------------- OUTPUT --------------------------=========== +############################################################################ + +########################## +# statistics filename add +########################## +OutputName Output_data + +##################################### +# enable, frequency +##################################### +RestartFreq true 10 +CheckpointFreq true 10 +CoordinatesFreq true 10 +ConsoleFreq true 10 +BlockAverageFreq true 10 +HistogramFreq true 10 + +DCDRestartFreq true 10 + +################################ +# OutHistSettings +################################ +DistName dis +HistName his +RunNumber 1 +RunLetter a +SampleFreq 100 + +################################## +# enable: blk avg., fluct. +################################## +OutEnergy true true +OutPressure true true +OutMolNum true true +OutDensity true true +OutVolume true true +OutSurfaceTention false false + diff --git a/test/input/GOMC_water_FF.inp b/test/input/GOMC_water_FF.inp new file mode 100644 index 000000000..7a724d3bb --- /dev/null +++ b/test/input/GOMC_water_FF.inp @@ -0,0 +1,2332 @@ +*>>>> CHARMM36 All-Hydrogen Parameter File for Proteins <<<<<<<<<< +*>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<<< +*>>>>>>>>>>>>>>>>>>>>>>>>>> Feb. 2012 <<<<<<<<<<<<<<<<<<<<<<<<<<<< +* All comments to the CHARMM web site: www.charmm.org +* parameter set discussion forum +* + +!references +! +!Robert B. Best, R.B., Xiao Zhu, X., Shim, J., Lopes, P. +!Mittal, J., Feig, M. and MacKerell, A.D., Jr. Optimization of the +!additive CHARMM all-atom protein force field targeting improved +!sampling of the backbone phi, psi and sidechain chi1 and chi2 +!dihedral angles. In preparation +! +!MacKerell, A.D., Jr., Feig, M. and Brooks, III, C.L. "Improved +!treatment of the protein backbone in empirical force fields," Journal +!of the American Chemical Society, 126: 698-699, 2004 +! +!MacKerell, Jr., A. D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R.L.; +!Evanseck, J.D.; Field, M.J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; +!Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.T.K.; Mattos, +!C.; Michnick, S.; Ngo, T.; Nguyen, D.T.; Prodhom, B.; Reiher, III, +!W.E.; Roux, B.; Schlenkrich, M.; Smith, J.C.; Stote, R.; Straub, J.; +!Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom +!empirical potential for molecular modeling and dynamics Studies of +!proteins. Journal of Physical Chemistry B, 1998, 102, 3586-3616. + +ATOMS +MASS -1 H 1.00800 ! polar H +MASS -1 HC 1.00800 ! N-ter H +MASS -1 HA 1.00800 ! nonpolar H +MASS -1 HP 1.00800 ! aromatic H +MASS -1 HB1 1.00800 ! backbone H +MASS -1 HB2 1.00800 ! aliphatic backbone H, to CT2 +MASS -1 HR1 1.00800 ! his he1, (+) his HG,HD2 +MASS -1 HR2 1.00800 ! (+) his HE1 +MASS -1 HR3 1.00800 ! neutral his HG, HD2 +MASS -1 HS 1.00800 ! thiol hydrogen +MASS -1 HE1 1.00800 ! for alkene; RHC=CR +MASS -1 HE2 1.00800 ! for alkene; H2C=CR +MASS -1 HA1 1.00800 ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 HA2 1.00800 ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 HA3 1.00800 ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str) +MASS -1 C 12.01100 ! carbonyl C, peptide backbone +MASS -1 CA 12.01100 ! aromatic C +MASS -1 CT 12.01100 ! aliphatic sp3 C, new LJ params, no hydrogens, see retinol stream file for parameters +MASS -1 CT1 12.01100 ! aliphatic sp3 C for CH +MASS -1 CT2 12.01100 ! aliphatic sp3 C for CH2 +MASS -1 CT2A 12.01100 ! from CT2 (GLU, HSP chi1/chi2 fitting) 05282010, zhu +MASS -1 CT3 12.01100 ! aliphatic sp3 C for CH3 +MASS -1 CPH1 12.01100 ! his CG and CD2 carbons +MASS -1 CPH2 12.01100 ! his CE1 carbon +MASS -1 CPT 12.01100 ! trp C between rings +MASS -1 CY 12.01100 ! TRP C in pyrrole ring +MASS -1 CP1 12.01100 ! tetrahedral C (proline CA) +MASS -1 CP2 12.01100 ! tetrahedral C (proline CB/CG) +MASS -1 CP3 12.01100 ! tetrahedral C (proline CD) +MASS -1 CC 12.01100 ! carbonyl C, asn,asp,gln,glu,cter,ct2 +MASS -1 CD 12.01100 ! carbonyl C, pres aspp,glup,ct1 +MASS -1 CS 12.01100 ! thiolate carbon +MASS -1 CE1 12.01100 ! for alkene; RHC=CR +MASS -1 CE2 12.01100 ! for alkene; H2C=CR +MASS -1 CAI 12.01100 ! aromatic C next to CPT in trp +MASS -1 N 14.00700 ! proline N +MASS -1 NR1 14.00700 ! neutral his protonated ring nitrogen +MASS -1 NR2 14.00700 ! neutral his unprotonated ring nitrogen +MASS -1 NR3 14.00700 ! charged his ring nitrogen +MASS -1 NH1 14.00700 ! peptide nitrogen +MASS -1 NH2 14.00700 ! amide nitrogen +MASS -1 NH3 14.00700 ! ammonium nitrogen +MASS -1 NC2 14.00700 ! guanidinium nitrogen +MASS -1 NY 14.00700 ! TRP N in pyrrole ring +MASS -1 NP 14.00700 ! Proline ring NH2+ (N-terminal) +MASS -1 O 15.99900 ! carbonyl oxygen +MASS -1 OB 15.99900 ! carbonyl oxygen in acetic acid +MASS -1 OC 15.99900 ! carboxylate oxygen +MASS -1 OH1 15.99900 ! hydroxyl oxygen +MASS -1 OS 15.99940 ! ester oxygen +MASS -1 S 32.06000 ! sulphur +MASS -1 SM 32.06000 ! sulfur C-S-S-C type +MASS -1 SS 32.06000 ! thiolate sulfur + + +BONDS + +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 All constants from Charmm +OT HT 99999999999 1.0000 ! SPC bond length + + +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 +! +NH2 CT1 240.000 1.4550 ! From LSN NH2-CT2 +! +!Indole/Tryptophan +CA CAI 305.000 1.3750 ! from CA CA +CAI CAI 305.000 1.3750 ! atm, methylindole, fit CCDSS +CPT CA 300.000 1.3600 ! atm, methylindole, fit CCDSS +CPT CAI 300.000 1.3600 ! atm, methylindole, fit CCDSS +CPT CPT 360.000 1.3850 ! atm, methylindole, fit CCDSS +CY CA 350.000 1.3650 ! trj, adm jr., 5/08/91, indole CCDB structure search +CY CAI 350.000 1.3650 ! from CY CA +CY CPT 350.000 1.4300 ! atm, methylindole, fit CDS data +CY CT3 375.000 1.4920 ! atm, methylindole, fit CDS data +CY CT2 375.000 1.4920 ! atm, methylindole, fit CDS data +HP CAI 340.000 1.0800 ! from HP CA +HP CY 350.000 1.0800 ! trp, adm jr., 12/30/91 +NY CA 270.000 1.3700 ! trp, adm jr., 12/30/91 +NY CPT 270.000 1.3700 ! atm, methylindole, from CCDS 1/17/04 +NY H 537.500 0.9760 ! atm, methylindole, 1/17/04 +CA CA 305.000 1.3750 ! ALLOW ARO + ! benzene, JES 8/25/89 +CE1 CE1 440.000 1.3400 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CE2 500.000 1.3420 ! + ! for propene, yin/adm jr., 12/95 +CE1 CT2 365.000 1.5020 ! + ! for butene; from propene, yin/adm jr., 12/95 +CE1 CT3 383.000 1.5040 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE2 510.000 1.3300 ! + ! for ethene, yin/adm jr., 12/95 +CP1 C 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CC 250.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 CD 200.000 1.4900 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 222.500 1.5270 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 222.500 1.5370 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPH1 CPH1 410.000 1.3600 ! ALLOW ARO + ! histidine, adm jr., 6/27/90 +CT1 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT1 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT1 222.500 1.5000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT2 CA 230.000 1.4900 ! ALLOW ALI ARO + ! phe,tyr, JES 8/25/89 +CT2 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT2 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 C 250.000 1.4900 ! ALLOW ALI PEP POL ARO + ! Ala Dipeptide ab initio calc's (LK) fixed from 10/90 (5/91) +CT3 CA 230.000 1.4900 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +CT3 CC 200.000 1.5220 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT3 CD 200.000 1.5220 ! ALLOW POL + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CPH1 229.630 1.5000 ! ALLOW ARO + ! his, adm jr., 7/22/89, FC from CT2CT, BL from crystals +CT3 CS 190.000 1.5310 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +CT3 CT1 222.500 1.5380 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 222.500 1.5280 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT3 222.500 1.5300 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +H CD 330.000 1.1100 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA1 CC 317.130 1.1000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +HA2 CP2 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 309.000 1.1110 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CS 300.000 1.1110 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CS 300.000 1.1110 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA1 CT1 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA2 CT2 309.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA3 CT3 322.000 1.1110 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +!HA CY 330.000 1.0800 ! ALLOW ARO + ! JWK 05/14/91 new r0 from indole +HE1 CE1 360.500 1.1000 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 365.000 1.1000 ! + ! for ethene, yin/adm jr., 12/95 +HB1 CP1 330.000 1.0800 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CT1 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +!HB3 CT3 330.000 1.0800 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HP CA 340.000 1.0800 ! ALLOW ARO + ! phe,tyr JES 8/25/89 +HR1 CPH1 375.000 1.0830 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 340.000 1.0900 ! ALLOW ARO + ! his, adm jr., 6/28/29 +HR2 CPH2 333.000 1.0700 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR3 CPH1 365.000 1.0830 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +N C 260.000 1.3000 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 320.000 1.4340 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 320.000 1.4550 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C 450.000 1.3650 ! ALLOW PEP POL ARO + ! mp2/6-311g** mgua vib. data, adm jr., 1/04 +NC2 CT2 390.000 1.4900 ! ALLOW ALI POL + ! mp2/6-311g** mgua vib. data, adm jr., 1/04 +NC2 CT3 390.000 1.4900 ! ALLOW ALI POL + ! mp2/6-311g** mgua vib. data, adm jr., 1/04 +NC2 HC 455.000 1.0000 ! ALLOW POL + ! 405.0->455.0 GUANIDINIUM (KK) +NH1 C 370.000 1.3450 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT2 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 CT3 320.000 1.4300 ! ALLOW ALI PEP POL ARO + ! NMA Gas & Liquid Phase IR Spectra (LK) +NH1 H 440.000 0.9970 ! ALLOW PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 HC 405.000 0.9800 ! ALLOW PEP POL ARO + ! (DS) +NH2 CC 430.000 1.3600 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +NH2 CT2 240.000 1.4550 + ! from NH2 CT3, neutral glycine, adm jr. +NH2 CT3 240.000 1.4550 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH2 H 480.000 1.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 HC 460.000 1.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT3 200.000 1.4800 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 HC 403.000 1.0400 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 320.000 1.4850 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 320.000 1.5020 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP HC 460.000 1.0060 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NR1 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH2 400.000 1.3600 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 H 466.000 1.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 400.000 1.3800 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 400.000 1.3200 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 380.000 1.3700 ! ALLOW ARO + ! his, adm jr., 6/28/90 +NR3 CPH2 380.000 1.3200 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 H 453.000 1.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +O C 620.000 1.2300 ! ALLOW PEP POL ARO + ! Peptide geometry, condensed phase (LK) +O CC 650.000 1.2300 ! ALLOW PEP POL ARO + ! adm jr. 4/10/91, acetamide +OB CC 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid vibrations and geom. +OB CD 750.000 1.2200 ! ALLOW PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 8/27/91, phenoxide +OC CC 525.000 1.2600 ! ALLOW PEP POL ARO ION + ! adm jr. 7/23/91, acetic acid +OC CT2 450.000 1.3300 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 450.000 1.3300 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA 334.300 1.4110 ! ALLOW ARO ALC + ! MeOH, EMB 10/10/89, +OH1 CD 230.000 1.4000 ! ALLOW PEP POL ARO ALC + ! adm jr. 5/02/91, acetic acid pure solvent +OH1 CT1 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT2 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 CT3 428.000 1.4200 ! ALLOW ALI ALC ARO + ! methanol vib fit EMB 11/21/89 +OH1 H 545.000 0.9600 ! ALLOW ALC ARO + ! EMB 11/21/89 methanol vib fit +OS CD 150.000 1.3340 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +OS CT3 340.000 1.4300 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +S CT2 198.000 1.8180 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S CT3 240.000 1.8160 ! ALLOW ALI SUL ION + ! fitted to C-S s 9/26/92 (FL) +S HS 275.000 1.3250 ! ALLOW SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +SM CT2 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC surface in DMDS 5/15/92 (FL) +SM CT3 214.000 1.8160 ! ALLOW SUL ION + ! improved CSSC surface in DMDS 5/15/92 (FL) +SM SM 173.000 2.0290 ! ALLOW SUL ION + ! improved CSSC surface in DMDS 5/15/92 (FL) +SS CS 205.000 1.8360 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HR1 CD 330.000 1.1100 ! acetaldehyde, benzaldehyde, 3ALP +O CD 720.000 1.2050 ! acetaldehyde, benzaldehyde, 3ALP. from stream/toppar_all27_na_bkb_modifications.str +CT2A CT1 222.500 1.5380 ! from CT2 CT1, Zhu +CT2 CT2A 222.500 1.5300 ! from CT2 CT2, Zhu +CT2A HA2 309.000 1.1110 ! from HA2 CT2, Zhu +CT2A CPH1 229.630 1.5000 ! from CT2 CPH1, Zhu +!ASP, CT2->CT2A +CT2A CC 200.000 1.5220 ! from CT2 CC, jshim +! RESI CYSM and PRES CYSD +CT1 CS 190.000 1.5380 ! from CT3 CS but lengthened; compare CT3 CT2 with CT2 CT1; kevo + +ANGLES + +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +HT OT HT 99999999999 109.5 0.0 0.0 ! water + +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!V(Urey-Bradley) = Kub(S - S0)**2 +! +!Ktheta: kcal/mole/rad**2 +!Theta0: degrees +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +H NH2 CT1 50.000 111.00 ! From LSN HC-NH2-CT2 +H NH2 CT2 50.000 111.00 ! From LSN HC-NH2-CT2, Neutral Gly Nterminus +NH2 CT1 CT1 67.700 110.00 ! From LSN NH2-CT2-CT2 +NH2 CT1 CT2 67.700 110.00 ! From LSN NH2-CT2-CT2 +NH2 CT1 CT2A 67.700 110.00 ! From LSN NH2-CT2-CT2 +NH2 CT1 CT3 67.700 110.00 ! From LSN NH2-CT2-CT2 +CT1 CD OH1 55.000 110.50 ! From ASPP CT2-CD-OH1 +CT3 CT1 CD 52.000 108.00 ! Ala cter +NH2 CT1 HB1 38.000 109.50 50.00 2.1400 ! From LSN NH2-CT2-HA +NH2 CT1 C 50.000 107.00 ! From ALA Dipep. NH1-CT2-C +NH2 CT1 CD 50.000 107.00 ! From ALA Dipep. NH1-CT2-C +NH2 CT2 C 50.000 107.00 ! From ALA Dipep. NH1-CT2-C, Neutral Gly Nterminus +!NH2 CT2 CD 50.000 107.00 ! From ALA Dipep. NH1-CT2-C, Neutral Gly Nterminus, repeat, see below +HB2 CT1 HB2 36.000 115.00 ! from HB2 CT2 HB2 +HB2 CT1 CD 50.000 109.50 ! from HB2 CT2 CD +NH1 CT1 HB2 48.000 108.00 ! from NH1 CT2 HB2 + +! +!Indole/Tryptophan +CAI CAI CA 40.000 120.00 35.00 2.41620 ! from CA CA CA +CAI CA CA 40.000 120.00 35.00 2.41620 ! from CA CA CA +CPT CA CA 50.000 113.20 ! atm, methylindole, 1/17/04 +CPT CPT CA 50.000 110.00 ! atm, methylindole, 1/17/04 +CPT CAI CA 50.000 113.20 ! atm, methylindole, 1/17/04 +CPT CPT CAI 50.000 110.00 ! atm, methylindole, 1/17/04 +CPT CY CA 85.000 106.40 25.00 2.26100 ! atm, methylindole, 1/17/04 +CPT NY CA 85.000 112.00 ! atm, methylindole, 1/17/04 +CT2 CY CA 30.000 127.00 ! atm, methylindole, CT3 CY CA +CT2 CY CPT 30.000 126.70 ! atm, methylindole, 1/17/04 +CT3 CY CA 30.000 127.00 ! atm, methylindole, CT3 CY CA +CT3 CY CPT 30.000 126.70 ! atm, methylindole, 1/17/04 +CY CPT CA 130.000 133.50 ! atm, methylindole, 1/17/04 +CY CPT CAI 130.000 133.50 ! atm, methylindole, 1/17/04 +CY CPT CPT 85.000 108.00 ! atm, methylindole, 1/17/04 +CY CT2 CT1 58.350 114.00 ! from TRP crystal, JWK +CY CT2 CT3 58.350 114.00 ! from TRP crystal, JWK +H NY CA 28.000 126.00 ! trp, adm jr., 12/30/91 +H NY CAI 28.000 126.00 ! trp, adm jr., 12/30/91 +H NY CPT 28.000 126.00 ! trp, adm jr., 12/30/91 +HA2 CT2 CY 55.000 109.50 ! atm, methylindole, 1/17/04 +HA3 CT3 CY 55.000 109.50 ! atm, methylindole, 1/17/04 +HP CA CAI 30.000 120.00 22.00 2.15250 ! from HP CA CA +HP CAI CA 30.000 120.00 22.00 2.15250 ! from HP CA CA +HP CA CPT 30.000 122.00 22.00 2.14600 ! trp, adm jr., 12/30/91 +HP CAI CPT 30.000 122.00 22.00 2.14600 ! from HP CA CPT +HP CA CY 32.000 125.00 25.00 2.17300 ! JWK 05/14/91 new theta0 and r0UB from indole +HP CY CA 32.000 126.40 25.00 2.18600 ! trp, adm jr., 12/30/91 +HP CY CPT 32.000 126.40 25.00 2.25500 ! JWK 05/14/91 new theta0 and r0UB from indole +NY CA CY 85.000 110.50 25.00 2.24000 ! trp, adm jr., 12/30/91 +NY CA HP 32.000 125.00 25.00 2.17700 ! JWK 05/14/91 new theta0 and r0UB from indole +NY CPT CA 130.000 129.50 ! atm, methylindole, 1/17/04 +NY CPT CAI 130.000 129.50 ! atm, methylindole, 1/17/04 +NY CPT CPT 95.000 107.40 ! atm, methylindole, 1/17/04 +CA CA CA 40.000 120.00 35.00 2.41620 ! ALLOW ARO + ! JES 8/25/89 +CE1 CE1 CT2 48.00 123.50 ! + ! for 2-butene, yin/adm jr., 12/95 +CE1 CE1 CT3 48.00 123.50 ! + ! for 2-butene, yin/adm jr., 12/95 +CE1 CT2 CT3 32.00 112.20 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT2 48.00 126.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +CE2 CE1 CT3 47.00 125.20 ! + ! for propene, yin/adm jr., 12/95 +CP1 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 C 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CC 52.000 112.3000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 CD 50.000 112.3000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP2 CP1 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 CP2 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C 60.000 117.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 100.000 114.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 100.000 111.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPH2 NR1 CPH1 130.000 107.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR2 CPH1 130.000 104.0000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CPH2 NR3 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CT1 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT1 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 6/27/2012, for Thr with CT1 patch +CT1 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT1 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT1 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT1 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT1 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT1 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT1 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +CT2 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT2 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT2 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2A CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT1 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2 CT1 CT1 53.350 111.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT2 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! from CT2 CT1 C, for lactams, adm jr. +CT2 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT3 CT2 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +CT2 CT2 CD 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +CT2A CT2 CD 52.000 108.0000 ! for GLUP, ZHU +CT2 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 CT2 CT2 58.350 113.60 11.16 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT2 CT3 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT2 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! 107.5->120.0 to make planar Arg (KK) +CT2 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT2 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 CA CA 45.800 122.3000 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +CT3 CPH1 CPH1 45.800 130.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC=>CT2CA CA,BA=> CRYSTALS +CT3 CT1 C 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +CT3 CT1 CC 52.000 108.0000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/09/92, for ALA cter +CT3 CT1 CT1 53.350 108.50 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT2 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT1 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CA 51.800 107.5000 ! ALLOW ALI ARO + ! ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CPH1 58.350 113.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2CT, U-B omitted +CT3 CT2 CT1 58.350 113.50 11.16 2.56100 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +CT3 CT2 CT2 58.000 115.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 CT2 CT3 53.350 114.00 8.00 2.56100 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CT3 NC2 C 62.300 120.0000 ! ALLOW ALI POL PEP ARO + ! methylguanidinium, adm jr., 3/26/92 +CT3 NH1 C 50.000 120.0000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +CT3 OS CD 40.000 109.60 30.00 2.26510 ! ALLOW POL PEP + ! adm jr. 5/02/91, acetic acid pure solvent +CT3 S CT2 34.000 95.0000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +H NH1 C 34.000 123.0000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +H NH1 CT1 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT2 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH1 CT3 35.000 117.0000 ! ALLOW PEP POL ARO ALI + ! NMA Vibrational Modes (LK) +H NH2 CC 50.000 120.0000 ! ALLOW POL PEP ARO + ! his, adm jr. 8/13/90 acetamide geometry and vibrations +H NH2 H 23.000 120.0000 ! ALLOW POL + ! adm jr. 8/13/90 acetamide geometry and vibrations +H NR1 CPH1 30.000 125.50 20.00 2.15000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR1 CPH2 30.000 127.00 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 25.000 126.00 15.00 2.13000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH2 25.000 126.00 15.00 2.09000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H OH1 CA 65.000 108.0000 ! ALLOW ALC ARO + ! JES 8/25/89 phenol +H OH1 CD 55.000 115.0000 ! ALLOW ALC ARO PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H OH1 CT1 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +H OH1 CT2 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +H OH1 CT3 57.500 106.0000 ! ALLOW ALC ARO ALI + ! methanol vib fit EMB 11/21/89 +HA2 CP2 CP1 33.430 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP2 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP2 CP3 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP2 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 CP2 26.500 110.10 22.53 2.17900 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CS CT3 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA2 CS HA2 35.500 108.40 14.00 1.77500 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CS HA3 35.500 108.40 14.00 1.77500 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA1 CT1 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA1 CT1 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA1 CT1 CT1 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA1 CT1 CT2 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA1 CT1 CT3 34.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA1 CT1 HA1 35.500 109.00 5.40 1.80200 ! TEST for test cpd + ! based on HA CT2 HA +HA2 CT2 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA2 CT2 CA 49.300 107.5000 ! ALLOW ALI ARO + ! PARALLH19 (JES) +HA2 CT2 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA2 CT2 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA2 CT2 CE1 45.00 111.50 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HA2 CT2 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA2 CT2 CT1 26.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA2 CT2 CT2 26.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA2 CT2 CT3 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA2 CT2 HA2 35.500 109.00 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA3 CT3 C 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! alanine dipeptide, LK, replaced, adm jr., 5/09/91 +HA3 CT3 CA 49.300 107.5000 ! ALLOW ALI ARO + ! toluene, adm jr. 3/7/92 +HA3 CT3 CC 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HA3 CT3 CD 33.000 109.50 30.00 2.16300 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +HA3 CT3 CE1 42.00 111.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HA3 CT3 CPH1 33.430 109.5000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, from CT2CT2HA, U-B OMITTED +HA3 CT3 CS 34.600 110.10 22.53 2.17900 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CT3 CT1 33.430 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane frequencies (MJF), alkane geometries (SF) +HA3 CT3 CT2 34.600 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA3 CT3 CT3 37.500 110.10 22.53 2.17900 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HA3 CT3 HA3 35.500 108.40 5.40 1.80200 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +HE1 CE1 CE1 52.00 119.50 ! + ! for 2-butene, yin/adm jr., 12/95 +HE1 CE1 CE2 42.00 118.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 40.00 116.00 ! + ! for 1-butene; from propene, yin/adm jr., 12/95 +HE1 CE1 CT3 22.00 117.00 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 CE1 45.00 120.50 ! + ! for propene, yin/adm jr., 12/95 +HE2 CE2 CE2 55.50 120.50 ! + ! for ethene, yin/adm jr., 12/95 +HE2 CE2 HE2 19.00 119.00 ! + ! for propene, yin/adm jr., 12/95 +HB1 CP1 C 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 CC 50.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 CD 50.000 112.0000 ! ALLOW PEP POL PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 CP2 35.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CT1 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB1 CT1 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB1 CT1 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB1 CT1 CT1 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB1 CT1 CT2 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB1 CT1 CT3 35.000 111.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 C 50.000 109.5000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 CC 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +HB2 CT2 CD 50.000 109.5000 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +HB2 CT2 HB2 36.000 115.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NC2 C 49.000 120.0000 ! ALLOW POL PEP ARO + ! 35.3->49.0 GUANIDINIUM (KK) +HC NC2 CT2 40.400 120.0000 ! ALLOW POL ALI + ! 107.5->120.0 to make planar Arg (KK) +HC NC2 CT3 40.400 120.0000 ! ALLOW POL ALI + ! methylguanidinium, adm jr., 3/26/92 +HC NC2 HC 25.000 120.0000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH2 CT2 50.000 111.0000 ! ALLOW POL + ! from HC NH2 CT3, neutral glycine, adm jr. +HC NH2 CT3 50.000 111.0000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +HC NH2 HC 39.000 106.5000 ! ALLOW POL + ! 40.0->25.0 GUANIDINIUM (KK) +HC NH3 CT1 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT2 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 CT3 30.000 109.50 20.00 2.07400 ! ALLOW POL ALI + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NH3 HC 44.000 109.5000 ! ALLOW POL + ! new stretch and bend; methylammonium (KK 03/10/92) +HC NP CP1 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 33.000 109.50 4.00 2.05600 ! ALLOW POL ALI PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP HC 51.000 107.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA 30.000 120.00 22.00 2.15250 ! ALLOW ARO + ! JES 8/25/89 benzene +HR1 CPH1 CPH1 22.000 130.00 15.00 2.21500 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 CPH1 CPH1 25.000 130.00 20.00 2.20000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS S CT2 38.800 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 43.000 95.0000 ! ALLOW SUL ION ALI + ! methanethiol pure solvent, adm jr., 6/22/92 +N C CP1 20.000 112.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 20.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 C 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CC 50.000 108.2000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CD 50.000 108.2000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 CP2 70.000 110.8000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP1 HB1 48.000 112.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 CP2 70.000 110.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CP3 HA2 48.000 108.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 C NC2 40.000 120.00 70.00 2.31 + ! mp2/6-311g** mgua vib data, adm jr., 1/04 + ! N-N distances: 2.29001, 2.31146, 2.33240 +NC2 CT2 CT2 67.700 107.5000 ! ALLOW ALI POL + ! arg, (DS) +NC2 CT2 HA2 56.500 107.5000 ! ALLOW ALI POL + ! mp2/6-311g** mgua vib data, adm jr., 1/04 +NC2 CT3 HA3 56.5000 107.5000 ! ALLOW ALI POL + ! mp2/6-311g** mgua vib data, adm jr., 1/04 +NH1 C CP1 80.000 116.5000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C CT2 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 C CT3 80.000 116.5000 ! ALLOW ALI PEP POL ARO + ! NMA Vib Modes (LK) +NH1 CT1 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH1 CT1 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT1 CT1 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 CT3 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT1 HB1 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT2 C 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT2 CC 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/20/92, for asn,asp,gln,glu and cters +NH1 CT2 CD 50.000 107.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH1 CT2 CT2 70.000 113.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT1 CT2, for lactams, adm jr. +NH1 CT2 HA2 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! from NH1 CT3 HA, for lactams, adm jr. +NH1 CT2 HB2 48.000 108.0000 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 CT3 HA3 51.500 109.5000 ! ALLOW ALI PEP POL ARO + ! NMA crystal (JCS) +NH2 CC CP1 80.000 112.5000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT1 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT2 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC CT3 50.000 116.50 50.00 2.45000 ! ALLOW ALI PEP POL ARO + ! adm jr. 8/13/90 acetamide geometry and vibrations +NH2 CC HA1 44.000 111.00 50.00 1.98000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +NH2 CT2 HB2 38.000 109.50 50.00 2.14000 + !from NH2 CT3 HA, neutral glycine, adm jr. +NH2 CT2 CD 52.000 108.0000 + !from CT2 CT2 CD, neutral glycine, adm jr. +NH2 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL + !from NH3 CT2 CT2, neutral lysine +NH2 CT2 HA2 38.000 109.50 50.00 2.14000 + !from NH2 CT3 HA, neutral lysine +NH2 CT3 HA3 38.000 109.50 50.00 2.14000 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +NH3 CT1 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT1 CT1 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT2 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 CT3 67.700 110.0000 ! ALLOW ALI POL + ! new aliphatics, adm jr., 2/3/92 +NH3 CT1 HB1 51.500 107.5000 ! ALLOW ALI POL PEP + ! new aliphatics, adm jr., 2/3/92 +NH3 CT2 C 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! alanine (JCS) +NH3 CT2 CC 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +NH3 CT2 CD 43.700 110.0000 ! ALLOW PEP POL ARO ALI + ! adm jr. 5/02/91, acetic acid pure solvent +NH3 CT2 CT2 67.700 110.0000 ! ALLOW ALI POL + ! methylammonium +NH3 CT2 CT3 67.700 110.0000 ! ALLOW ALI POL + ! ethylammonium +NH3 CT2 HA2 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NH3 CT2 HB2 51.500 107.5000 ! ALLOW ALI POL PEP + ! for use on NTER -- from NH3 CT2HA (JCS) -- (LK) +NH3 CT3 HA3 45.000 107.50 35.00 2.10100 ! ALLOW ALI POL + ! new stretch and bend; methylammonium (KK 03/10/92) +NP CP1 C 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC 50.000 106.0000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CD 50.000 106.0000 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 HB1 51.500 107.5000 ! ALLOW ALI POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 CP2 70.000 108.5000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP3 HA2 51.500 109.1500 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NR1 CPH1 CPH1 130.000 106.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR1 CPH1 CT2 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 CT3 45.800 124.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR1 CPH1 HR3 25.000 124.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH2 HR1 25.000 122.50 20.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH1 CPH1 130.000 110.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CT2 45.800 120.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR2 CPH1 HR3 25.000 120.00 20.00 2.14000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH2 HR1 25.000 125.00 20.00 2.12000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR2 CPH2 NR1 130.000 112.5000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CT2 45.800 122.0000 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FC FROM CA CT2CT +NR3 CPH1 HR1 22.000 122.00 15.00 2.18000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 HR2 32.000 126.00 25.00 2.14000 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH2 NR3 145.000 108.0000 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +O C CP1 80.000 118.0000 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C CT3 80.000 121.0000 ! ALLOW ALI PEP POL ARO + ! Alanine Dipeptide ab initio calc's (LK) +O C H 50.000 121.7000 ! ALLOW PEP POL ARO + ! acetaldehyde (JCS) +O C N 80.000 122.5000 ! ALLOW PRO PEP POL ARO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 80.000 122.5000 ! ALLOW PEP POL ARO + ! NMA Vib Modes (LK) +O CC CP1 80.000 118.0000 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT1 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT2 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC CT3 15.000 121.00 50.00 2.44000 ! ALLOW ALI PEP POL ARO + ! adm jr. 4/10/91, acetamide update +O CC HA1 44.000 122.0000 ! ALLOW POL + ! adm jr., 5/13/91, formamide geometry and vibrations +O CC NH2 75.000 122.50 50.00 2.37000 ! ALLOW POL PEP ARO + ! adm jr. 4/10/91, acetamide update +OB CD CP1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OB CD CT1 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT2 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OB CD CT3 70.000 125.00 20.00 2.44200 ! ALLOW ALI PEP POL ARO + ! adm jr. 5/02/91, acetic acid pure solvent +OC CA CA 40.000 120.0000 ! ALLOW POL ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT2 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC CT3 40.000 118.00 50.00 2.38800 ! ALLOW ALI PEP POL ARO ION + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CC OC 100.000 124.00 70.00 2.22500 ! ALLOW POL ION PEP ARO + ! adm jr. 7/23/91, correction, ACETATE (KK) +OC CT2 CT3 65.000 122.0000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT2 HA2 65.000 118.3000 ! ALLOW ALC + ! ethoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OC CT3 HA3 65.000 118.3000 ! ALLOW ALC + ! methoxide 6-31+G* geom/freq, adm jr., 6/1/92 +OH1 CA CA 45.200 120.0000 ! ALLOW ARO ALC + ! PARALLH19 WITH [122.3] (JES) +OH1 CD CT2 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD CT3 55.000 110.5000 ! ALLOW ALI PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CD OB 50.000 123.00 210.00 2.26200 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid vibrations +OH1 CT1 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT1 HA1 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT1 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT2 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 CT3 75.700 110.1000 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT2 HA2 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OH1 CT3 HA3 45.900 108.8900 ! ALLOW ALI ALC ARO + ! MeOH, EMB, 10/10/89 +OS CD CP1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OS CD CT1 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT2 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD CT3 55.000 109.00 20.00 2.32600 ! ALLOW POL PEP + ! adm jr., 4/05/91, for PRES CT1 from methylacetate +OS CD OB 90.000 125.90 160.00 2.25760 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OS CT2 HA2 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +OS CT3 HA3 60.000 109.5000 ! ALLOW PEP POL + ! adm jr. 4/05/91, for PRES CT1 from methyl acetate +S CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +S CT2 CT2 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 CT3 58.000 114.5000 ! ALLOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +S CT2 HA2 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +S CT3 HA3 46.100 111.3000 ! ALLOW ALI SUL ION + ! vib. freq. and HF/6-31G* geo. (DTN) 8/24/90 +SM CT2 CT1 58.000 112.5000 ! ALLOW ALI SUL ION + ! as in expt.MeEtS & DALC crystal, 5/15/92 +SM CT2 CT3 58.000 112.5000 ! ALLOW ALI SUL ION + ! diethyldisulfide, as in expt.MeEtS & DALC crystal, 5/15/92 +SM CT2 HA2 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM CT3 HA3 38.000 111.0000 ! ALLOW ALI SUL ION + ! new S-S atom type 8/24/90 +SM SM CT2 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 72.500 103.3000 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 55.000 118.0000 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +SS CS HA2 40.000 112.3000 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +SS CS HA3 40.000 112.3000 ! ALLOW SUL + ! methylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +O CD HR1 75.000 121.0000 ! acetaldehyde, benzaldehyde, 3ALP, retinal +!For GLU/HSP, Zhu +NH1 CT1 CT2A 70.000 113.5000 ! from NH1 CT1 CT2 +HB1 CT1 CT2A 35.000 111.0000 ! from HB1 CT1 CT2 +CT2A CT1 C 52.000 108.0000 ! from CT2 CT1 C +CT1 CT2A HA2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT1 +CT1 CT2A CT2 58.350 113.5000 11.16 2.56100 ! from CT2 CT2 CT1 +HA2 CT2A HA2 35.500 109.0000 5.40 1.80200 ! from HA2 CT2 HA2 +HA2 CT2A CT2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT2 +CT2A CT2 HA2 26.500 110.1000 22.53 2.17900 ! from HA2 CT2 CT2 +CT2A CT2 CC 52.000 108.0000 ! from CT2 CT2 CC +CT1 CT2A CPH1 58.350 113.0000 ! from CT1 CT2 CPH1 +HA2 CT2A CPH1 33.430 109.5000 ! from HA2 CT2 CPH1 +CT2A CPH1 CPH1 45.800 130.0000 ! from CT2 CPH1 CPH1 +CT2A CPH1 NR3 45.800 122.0000 ! from NR3 CPH1 CT2 +!ASP, CT2->CT2A, jshim +CT1 CT2A CC 52.000 108.0000 ! from CT1 CT2 CC +HA2 CT2A CC 33.000 109.5000 30.00 2.16300 ! from HA2 CT2 CC +OC CC CT2A 40.000 118.0000 50.00 2.38800 ! from OC CC CT2 +NH3 CT1 CT2A 67.700 110.0000 ! from NH3 CT1 CT2 +CT2A CT1 CD 52.000 108.0000 ! from CT2 CT1 CD +! RESI CYSM and PRES CYSD +NH2 CT1 CS 67.700 110.0000 ! from NH2 CT1 CT2 , kevo +CS CT1 C 52.000 108.0000 ! from CT2 CT1 C , kevo +CS CT1 CC 52.000 108.0000 ! from CT2 CT1 CC , kevo +CS CT1 CD 52.000 108.0000 ! from CT2 CT1 CD , kevo +HB1 CT1 CS 35.000 111.0000 ! from HB1 CT1 CT2 , kevo +NH1 CT1 CS 70.000 113.5000 ! from NH1 CT1 CT2 , kevo +NH3 CT1 CS 67.700 110.0000 ! from NH3 CT1 CT2 , kevo +SS CS CT1 55.000 118.0000 ! from SS CS CT3 , kevo +HA2 CS CT1 34.600 110.10 22.53 2.17900 ! from HA2 CS CT3 to be consistent with SS CS CT1, kevo +! PRES SERD +OC CT2 CT1 65.000 122.0000 ! from OC CT2 CT3 , kevo + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! +!Neutral N and C termini +NH2 CT1 C O 0.0000 1 0.00 +NH2 CT2 C O 0.0000 1 0.00 ! Neutral Gly Nterminus +NH2 CT1 C NH1 0.0000 1 0.00 +NH2 CT1 C N 0.0000 1 0.00 +NH2 CT2 C NH1 0.0000 1 0.00 ! Neutral Gly Nterminus +NH2 CT2 C N 0.0000 1 0.00 ! NNEU +NH2 CT1 CT2A HA2 0.2000 3 0.00 ! From X CT1 CT2 X +H NH2 CT1 CT1 0.0000 1 0.00 +H NH2 CT1 C 0.0000 1 0.00 +H NH2 CT1 CD 0.0000 1 0.00 +H NH2 CT2 C 0.0000 1 0.00 ! Neutral Gly Nterminus +H NH2 CT2 CD 0.0000 1 0.00 ! Neutral Gly Nterminus +H NH2 CT1 HB1 0.1100 3 0.00 ! From LSN HC-NH2-CT2-HA +H NH2 CT2 HB2 0.1100 3 0.00 ! From LSN HC-NH2-CT2-HA, Neutral Gly Nterminus +H NH2 CT1 CT2 0.1100 3 0.00 ! From LSN HC-NH2-CT2-CT2 +H NH2 CT1 CT2A 0.1100 3 0.00 ! From LSN HC-NH2-CT2-CT2 +H NH2 CT1 CT3 0.1100 3 0.00 ! From LSN HC-NH2-CT2-CT2 +CC CT2A CT1 NH2 0.6800 1 180.00 ! From CC CT2A CT1 NH1 +CC CT2A CT1 NH2 0.1000 2 180.00 +CC CT2A CT1 NH2 0.3800 3 0.00 +CD CT1 CT2A CC 1.6100 1 180.00 ! From C CT1 CT2A CC +CD CT1 CT2A CC 1.2900 2 180.00 +CD CT1 CT2A CC 0.5900 3 180.00 + +!Indole/Tryptophan +CAI CA CA CAI 3.1000 2 180.00 ! from CA CA CA CA +CA CPT CPT CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +CAI CPT CPT CAI 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +CA CY CPT CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +CA CY CPT CAI 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +CA NY CPT CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +CPT CA CA CA 3.0000 2 180.00 ! JWK 05/14/91 fit to indole +CPT CPT CA CA 3.0000 2 180.00 ! JWK 05/14/91 fit to indole +CA NY CPT CAI 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +CPT CAI CA CA 3.0000 2 180.00 ! JWK 05/14/91 fit to indole +CPT CPT CAI CA 3.0000 2 180.00 ! JWK 05/14/91 fit to indole +CPT CPT CY CA 5.0000 2 180.00 ! atm, methylindole, 1/17/04 +CPT CPT NY CA 6.5000 2 180.00 ! atm, methylindole, 1/17/04 +CT3 CY CPT CA 2.5000 2 180.00 ! atm, methylindole, r6r5 +CT3 CY CPT CAI 2.5000 2 180.00 ! atm, methylindole, r6r5 +CT3 CY CPT CPT 3.0000 2 180.00 ! atm, methylindole, meth +CT2 CY CPT CA 2.5000 2 180.00 ! atm, methylindole, r6r5 +CT2 CY CPT CAI 2.5000 2 180.00 ! atm, methylindole, r6r5 +CT2 CY CPT CPT 3.0000 2 180.00 ! atm, methylindole, meth +CY CA NY CPT 6.0000 2 180.00 ! atm, methylindole, 1/17/04 +CY CPT CA CA 4.0000 2 180.00 ! atm, methylindole, 1/17/04 +CY CPT CPT CA 4.0000 2 180.00 ! atm, methylindole, 1/17/04 +CY CPT CAI CA 4.0000 2 180.00 ! atm, methylindole, 1/17/04 +CY CPT CPT CAI 4.0000 2 180.00 ! atm, methylindole, 1/17/04 +H NY CA CY 0.0500 2 180.00 ! atm, methylindole, 1/17/04 +H NY CPT CA 0.2000 2 180.00 ! atm, methylindole, 1/17/04 +H NY CPT CAI 0.2000 2 180.00 ! atm, methylindole, 1/17/04 +H NY CPT CPT 0.8500 2 180.00 ! atm, methylindole, 1/17/04 +HP CAI CA CA 4.2000 2 180.00 ! from HP CA CA CA +HP CA CA CPT 3.0000 2 180.00 ! JWK 05/14/91 fit to indole +HP CA CPT CPT 3.0000 2 180.00 ! JWK indole 05/14/91 +HP CA CPT CY 4.0000 2 180.00 ! atm, methylindole, 1/17/04 +HP CA CA CAI 4.2000 2 180.00 ! from HP CA CA CA +HP CA CAI CPT 3.0000 2 180.00 ! from HP CA CA CPT +HP CAI CA HP 2.4000 2 180.00 ! from HP CA CA HP +HP CAI CPT CPT 3.0000 2 180.00 ! from HP CA CPT CPT +HP CAI CPT CY 4.0000 2 180.00 ! from HP CA CPT CY, r6r5 +HP CA CY CPT 2.8000 2 180.00 ! adm jr., 12/30/91, for jwk +HP CA CY CT3 1.2000 2 180.00 ! atm, methylindole +HP CA CY CT2 1.2000 2 180.00 ! atm, methylindole +HP CA NY CPT 2.6000 2 180.00 ! adm jr., 12/30/91, for jwk +HP CA NY H 0.4000 2 180.00 ! JWK 05/14/91 fit to indole +HP CY CA HP 1.0000 2 180.00 ! JWK 05/14/91 fit to indole +HP CY CPT CA 2.8000 2 180.00 ! JWK 05/14/91 fit to indole +HP CY CPT CAI 2.8000 2 180.00 ! JWK 05/14/91 fit to indole +HP CY CPT CPT 2.6000 2 180.00 ! JWK 05/14/91 fit to indole +NY CA CY CPT 5.0000 2 180.00 ! atm, methylindole, 1/17/04 +NY CA CY CT3 2.5000 2 180.00 ! atm, methylindole, from NY CA CY CT3 +NY CA CY CT2 2.5000 2 180.00 ! atm, methylindole, from NY CA CY CT3 +NY CA CY HP 3.5000 2 180.00 ! JWK indole 05/14/91 +NY CPT CA CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04, r6r5 +NY CPT CA HP 3.0000 2 180.00 ! JWK 05/14/91 fit to indole, r6r5 +NY CPT CPT CA 4.0000 2 180.00 ! atm, methylindole, 1/17/04, bfly +NY CPT CAI CA 3.0000 2 180.00 ! atm, methylindole, 1/17/04 +NY CPT CAI HP 3.0000 2 180.00 ! JWK 05/14/91 fit to indole, r6r5 +NY CPT CPT CAI 4.0000 2 180.00 ! atm, methylindole, 1/17/04, bfly +NY CPT CPT CY 6.5000 2 180.00 ! JWK 05/14/91 fit to indole, r5 t1 +CT3 CT2 CY CA 0.3800 2 0.00 ! trp, from ethylbenzene, adm jr., 3/7/92 +CT3 CT2 CY CPT 0.2500 2 180.00 ! atm 1/14/04 3-ethylindole +CT3 CT2 CY CPT 0.3000 3 0.00 ! atm 1/14/04 3-ethylindole +HA3 CT3 CY CA 0.0100 3 0.00 ! atm, methylindole, 1/17/04 +HA3 CT3 CY CPT 0.2000 3 0.00 ! atm, methylindole, 1/17/04 +HA2 CT2 CY CA 0.0100 3 0.00 ! atm, methylindole, 1/17/04 +HA2 CT2 CY CPT 0.2000 3 0.00 ! atm, methylindole, 1/17/04 +X CS SS X 0.0000 3 0.20 ! guess + !from methanethiol, HS S CT3 HA + !adm jr., 7/01 +C CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +C N CP1 C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CA CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 +!CA CT2 CT1 C 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CC CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CC CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +CC CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +!CC CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL +! ! Alanine dipeptide; NMA; acetate; etc. adm jr., 3/3/93c +CC CT2 NH1 C 2.0000 1 180.00 ! ALLOW PEP POL + ! Based on Gly3 data from graf et al, RB 7/1/11 +CD CP1 N C 0.0000 1 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CD CT1 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +!CD CT2 NH1 C 0.2000 1 180.00 ! ALLOW PEP POL +! ! Alanine dipeptide; NMA; acetate; etc. backbon adm jr., 3/3/93c +CD CT2 NH1 C 2.0000 1 180.00 ! ALLOW PEP POL + ! Based on Gly3 data from graf et al, RB 7/1/11 +CE1 CE1 CT3 HA3 0.0300 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT2 CT3 0.5000 1 180.00 ! + ! 1-butene, adm jr., 2/00 update +CE2 CE1 CT2 CT3 1.3000 3 180.00 ! + ! 1-butene, adm jr., 2/00 update +CE2 CE1 CT2 HA2 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +CE2 CE1 CT3 HA3 0.0500 3 180.00 ! + ! for propene, yin/adm jr., 12/95 +CP1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N C CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 C 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CC 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 N CP1 CP2 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CP3 NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CPH2 NR1 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR2 CPH1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CPH2 NR3 CPH1 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +CT1 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT1 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT1 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT1 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT1 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! from CT2 C NH1 CT2, adm jr. 10/21/96 +CT2 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +CT2 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT2 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR2 CPH2 +CT2 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +CT2 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT2 CT2 CPH1 CPH1 0.4000 1 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. ADM JR., 9/4/89 +!aliphatic chain parameters compatible with the revised side-chain parameters, from all22_carb>>all27_lip>>all31 + ! lower butane gauche conformer +CT2 CT2 CT2 CT2 0.10 2 180.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT2 0.15 4 0.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT2 0.10 6 180.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT3 0.10 2 180.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT3 0.15 4 0.00 ! alkane, 4/98, adm jr. +CT2 CT2 CT2 CT3 0.10 6 180.00 ! alkane, 4/98, adm jr. +! +CT2 CT2 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! from CT2 CT1 NH1 C, for lactams, adm jr. +CT2 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT2 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT2 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT2 SM SM CT2 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT2 SM SM CT2 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT2 SM SM CT2 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 C NH1 CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 C NH1 CT2 1.6000 1 0.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! for acetylated GLY N-terminus, adm jr. +CT3 C NH1 CT3 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +CT3 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +CT3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM HA CPH1 NR1 CPH2 +CT3 CT1 NH1 C 1.8000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +CT3 CT2 CA CA 0.2300 2 180.00 ! ALLOW ARO ALI + ! ethylbenzene ethyl rotation, adm jr. 3/7/92 +CT3 CT2 CPH1 CPH1 0.2000 1 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.2700 2 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-ethylimidazole 4-21G rot bar, adm jr. 3/4/92 +CT3 CT2 S CT3 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 CT2 S CT3 0.3700 3 0.00 ! ALOW ALI SUL ION + ! DTN 8/24/90 +CT3 NH1 C CP1 1.6000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +CT3 NH1 C CT1 1.6000 1 0.00 ! ALLOW PEP + ! Revised to adjust NMA cis/trans energy difference. (LK) +CT3 NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +CT3 S CT2 CT2 0.2400 1 180.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 S CT2 CT2 0.3700 3 0.00 ! ALOW ALI SUL ION + ! expt. MeEtS, 3/26/92 (FL) +CT3 SM SM CT3 1.0000 1 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +CT3 SM SM CT3 4.1000 2 0.00 ! ALLOW ALI SUL ION + ! mp 6-311G** dimethyldisulfide, 3/26/92 (FL) +CT3 SM SM CT3 0.9000 3 0.00 ! ALLOW ALI SUL ION + ! improved CSSC dihedral in DMDS 5/15/92 (FL) +H NH1 C CP1 2.5000 2 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NH1 C CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 C CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +H NH1 CT1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +H NH1 CT1 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH1 CT2 CC 0.0000 1 0.00 ! ALLOW PEP POL + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +H NH1 CT2 CD 0.0000 1 0.00 ! ALLOW PEP POL + ! adm jr. 5/02/91, acetic acid pure solvent +H NH1 CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from H NH1 CT2 CT3, for lactams, adm jr. +H NH1 CT2 CT3 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +H NH2 CC CT1 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT2 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CT3 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +H NH2 CC CP1 2.5000 2 180.00 ! ALLOW PEP POL ARO PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +H NR1 CPH1 CPH1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/20/89 +H NR1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HA CPH1 NR1 H +H NR3 CPH1 CPH1 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +H NR3 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H NR3 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 7/22/89, FROM HC NR3 CPH1 HA +H OH1 CA CA 0.9900 2 180.00 ! ALLOW ARO ALC + ! phenol OH rot bar, 3.37 kcal/mole, adm jr. 3/7/92 +H OH1 CT1 CT3 1.3300 1 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.1800 2 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT1 CT3 0.3200 3 0.00 ! ALLOW ALC + ! 2-propanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT2 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 1.3000 1 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.3000 2 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +H OH1 CT2 CT3 0.4200 3 0.00 ! ALLOW ALC + ! ethanol OH hf/6-31g* torsional surface, adm jr., 3/2/93 +HA1 CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL + ! adm jr. 4/10/91, acetamide update +HA2 CP3 N C 0.0000 3 180.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 N CP1 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA2 CP3 NP CP1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HA1 CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA2 CT2 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA2 CT2 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA2 CT2 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA2 CT2 S CT3 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +HA3 CT3 CPH1 CPH1 0.0000 3 0.00 ! ALLOW ARO + ! 4-methylimidazole 4-21G//6-31G* rot bar. adm jr., 9/4/89 +HA3 CT3 CS HA2 0.1600 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CT3 CS HA3 0.1600 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +HA3 CT3 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +HA3 CT3 NH1 C 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA3 CT3 NH1 H 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +HA3 CT3 S CT2 0.2800 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +HE1 CE1 CE1 HE1 1.0000 2 180.00 ! + ! 2-butene, adm jr., 8/98 update +CT3 CE1 CE1 HE1 1.0000 2 180.00 ! + ! 2-butene, adm jr., 8/98 update +HE1 CE1 CE2 HE2 5.2000 2 180.00 ! + ! for propene, yin/adm jr., 12/95 +HE1 CE1 CT2 HA2 0.0000 3 0.00 + ! butene, adm jr., 2/00 update +HE1 CE1 CT2 CT3 0.1200 3 0.00 ! + ! for butene, yin/adm jr., 12/95 +HE1 CE1 CT3 HA3 0.0000 3 0.00 + ! butene, adm jr., 2/00 update +HE2 CE2 CE1 CT2 5.2000 2 180.00 ! + ! for butene, yin/adm jr., 12/95 +HB1 CP1 N C 0.8000 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 N CP3 0.1000 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CP1 NP CP3 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HB1 CT1 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB1 CT1 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 NH1 C 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HB2 CT2 NH1 H 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +HC NH2 CT2 HB2 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NH2 CT2 CD 0.1100 3 0.00 + !from X CT3 NH2 X, neutral glycine, adm jr. +HC NH2 CT2 CT2 0.1100 3 0.00 + !from X CT3 NH2 X, neutral lysine +HC NH2 CT2 HA2 0.1100 3 0.00 + !from X CT3 NH2 X, neutral lysine +HC NP CP1 C 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CC 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CD 0.0800 3 0.00 ! ALLOW PRO PEP + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP1 HB1 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 CP2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HC NP CP3 HA2 0.0800 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +HP CA CA CA 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HP CA CA CT2 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 toluene and ethylbenzene +HP CA CA CT3 4.2000 2 180.00 ! ALLOW ARO + ! toluene, adm jr., 3/7/92 +HP CA CA HP 2.4000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 benzene +HR1 CPH1 CPH1 CT2 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 CT3 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 CPH1 HR1 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, his +HR1 CPH1 NR3 CPH2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH1 NR3 H 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR1 CPH2 NR2 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 CPH1 3.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +HR2 CPH2 NR3 H 0.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90, YES, 0.0 +HR3 CPH1 CPH1 CT2 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 CT3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 CPH1 HR3 2.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HR3 CPH1 NR2 CPH2 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS S CT2 CT3 0.2400 1 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.1500 2 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 CT3 0.2700 3 0.00 ! ALLOW ALI SUL ION + ! ethanethiol C-C-S-H surface, adm jr., 4/18/93 +HS S CT2 HA2 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +HS S CT3 HA3 0.2000 3 0.00 ! ALLOW ALI SUL ION + ! methanethiol pure solvent, adm jr., 6/22/92 +N C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB1 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT1 HB1 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT2 HB2 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N C CT3 HA3 0.0000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +N CT1 CT2 CA 0.0400 3 0.00 ! ALLOW ARO + ! 2.7 kcal/mole CH3 rot in ethylbenzene, adm jr, 3/7/92 +NH1 C CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB1 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 C CT1 CT1 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT2 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 CT3 0.0000 1 0.00 ! ALLOW PEP + ! ala dipeptide corrxn for new C VDW Rmin, 4/10/93 (LK) +NH1 C CT1 HB1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT1 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT2 CT2 0.0000 1 0.00 ! ALLOW PEP + ! from NH1 C CT1 CT2, for lactams, adm jr. +NH1 C CT2 HA2 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 C CT2 HB2 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +NH1 C CT2 NH1 0.6000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH1 C CT3 HA3 0.0000 3 0.00 ! ALLOW PEP + ! LK for autogenerate dihe, sp2-methyl, no dihedral potential +NH1 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH1 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB1 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH2 CC CT2 HA2 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +NH3 CT1 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NH3 CT1 C NH1 0.6000 1 0.00 ! ALLOW PEP PRO + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93 +NH3 CT1 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NH3 CT2 C N 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +!!!NH3 CT2 C NH1 0.4000 1 0.00 ! ALLOW PEP PRO +!!! ! adm jr. 3/24/92, for PRES GLYP +NH3 CT2 C NH1 1.0000 1 0.00 ! ALLOW PEP PRO + ! RB 1/07/11, based on graf et al Gly 3 N-ter J-couplings for PRES GLYP +NH3 CT2 CC NH2 0.4000 1 0.00 ! ALLOW PEP PRO + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +NP CP1 C N 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 C NH1 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NP CP1 CC NH2 0.3000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NR1 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR1 CPH1 CPH1 HA +NR1 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR1 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT2 HA2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH1 CT3 HA3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR1 CPH2 NR2 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH1 CPH1 CT2 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 CT3 3.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/22/89, FROM NR2 CPH1 CPH1 HA +NR2 CPH1 CPH1 HR3 3.0000 2 180.00 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +NR2 CPH1 CPH1 NR1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +!NR2 CPH1 CT2 CT1 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! HIS CB-CG TORSION, +NR2 CPH1 CT2 HA2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH1 CT3 HA3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR2 CPH2 NR1 CPH1 14.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR2 CPH2 NR1 H 1.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH1 CPH1 CT2 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 CT3 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 HR1 2.5000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CPH1 NR3 12.0000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +NR3 CPH1 CT2 CT2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 CT3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT2 HA2 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH1 CT3 HA3 0.1900 3 0.00 ! ALLOW ARO + ! 4-METHYLIMIDAZOLE 4-21G//6-31G* ROT BAR. ADM JR., 9/4/89 +NR3 CPH2 NR3 CPH1 12.0000 2 180.00 ! ALLOW ARO + ! his, ADM JR., 7/20/89 +NR3 CPH2 NR3 H 1.4000 2 180.00 ! ALLOW ARO + ! his, adm jr., 6/27/90 +O C CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB1 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C CT1 CT1 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT2 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 CT3 1.4000 1 0.00 ! ALLOW PEP + ! ala dipeptide update for new C VDW Rmin, adm jr., 3/3/93c +O C CT1 HB1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT1 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT2 CT2 1.4000 1 0.00 ! ALLOW PEP + ! from O C CT1 CT2, for lactams, adm jr. +O C CT2 HA2 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C CT2 HB2 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH1 0.0000 1 0.00 ! ALLOW PEP + ! Alanine Dipeptide ab initio calc's (LK) +O C CT2 NH3 0.0000 1 0.00 ! ALLOW PEP PRO + ! Backbone parameter set made complete RLD 8/8/90 +O C CT3 HA3 0.0000 3 180.00 ! ALLOW POL + ! adm jr., 8/13/90 acetamide geometry and vibrations +O C N CP1 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP1 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 2.7500 2 180.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C N CP3 0.3000 4 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O C NH1 CT1 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT2 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 CT3 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O C NH1 H 2.5000 2 180.00 ! ALLOW PEP + ! Gives appropriate NMA cis/trans barrier. (LK) +O CC CP1 CP2 0.4000 1 180.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 CP2 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB1 0.4000 1 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 HB1 0.6000 2 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CP1 N -0.3000 4 0.00 ! ALLOW PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +O CC CT2 HA2 0.0000 3 180.00 ! ALLOW POL + ! adm jr. 4/05/91, for asn,asp,gln,glu and cters +O CC NH2 H 1.4000 2 180.00 ! ALLOW PEP POL ARO PRO + ! adm jr. 4/10/91, acetamide update +OB CD OS CT2 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT2 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 0.9650 1 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OB CD OS CT3 3.8500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +OC CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! adm jr. 8/27/91, phenoxide +OC CC CP1 CP2 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 HB1 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 N 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CP1 NP 0.1600 3 0.00 ! ALLOW PEP PRO POL + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +OC CC CT1 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OC CC CT2 NH3 3.2000 2 180.00 ! ALLOW PEP PRO + ! adm jr. 4/17/94, zwitterionic glycine +OH1 CA CA CA 3.1000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +OH1 CA CA HP 4.2000 2 180.00 ! ALLOW ARO + ! JES 8/25/89 phenol +S CT2 CT2 HA2 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM CT2 CT2 HA2 0.0100 3 0.00 ! ALLOW ALI SUL ION + ! DTN 8/24/90 +SM SM CT2 CT1 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 CT2 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 CT3 0.3100 3 0.00 ! ALLOW SUL ALI + ! S-S for cys-cys, dummy parameter for now ... DTN 9/04/90 +SM SM CT2 HA2 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SM SM CT3 HA3 0.1580 3 0.00 ! ALLOW ALI SUL ION + ! expt. dimethyldisulfide, 3/26/92 (FL) +SS CS CT3 HA3 0.1500 3 0.00 ! ALLOW SUL + ! ethylthiolate 6-31+G* geom/freq, adm jr., 6/1/92 +X C NC2 X 2.2500 2 180.00 ! ALLOW PEP POL ARO + ! 9.0->2.25 GUANIDINIUM (KK) +X CD OH1 X 2.0500 2 180.00 ! ALLOW PEP POL ARO ALC + ! adm jr, 10/17/90, acetic acid C-Oh rotation barrier +X CD OS X 2.0500 2 180.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CE1 CE1 X 0.1500 1 0.00 + ! 2-butene, adm jr., 2/00 update +X CE1 CE1 X 8.5000 2 180.00 + ! 2-butene, adm jr., 2/00 update +X CE2 CE2 X 4.9000 2 180.00 ! + ! for ethene, yin/adm jr., 12/95 +X CP1 C X 0.0000 6 180.00 ! ALLOW POL PEP PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP1 CC X 0.0000 6 180.00 ! ALLOW POL PEP + ! changed to 0.0 RLD 5/19/92 +X CP1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! Alanine dipeptide; NMA; acetate; etc. backbone param. RLD 3/22/92 +X CP1 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP2 CP2 X 0.1600 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CP3 CP2 X 0.1400 3 0.00 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +X CT1 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT1 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT1 CT1 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT2 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 CT3 X 0.2000 3 0.00 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +X CT1 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT1 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT1 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT2 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT2 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT2 CT2 X 0.1900 3 0.00 ! ALLOW ALI + ! alkane, 4/98, yin and mackerell +X CT2 CT3 X 0.1600 3 0.00 ! ALLOW ALI + ! alkane, 4/98, yin and mackerell +X CT2 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT2 NH3 X 0.1000 3 0.00 ! ALLOW ALI POL + ! 0.715->0.10 METHYLAMMONIUM (KK) +X CT2 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT2 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CA X 0.0000 6 0.00 ! ALLOW ALI ARO + ! toluene, adm jr., 3/7/92 +X CT3 CC X 0.0500 6 180.00 ! ALLOW POL PEP + ! For side chains of asp,asn,glu,gln, (n=6) from KK(LK) +X CT3 CD X 0.0000 6 180.00 ! ALLOW POL PEP + ! adm jr. 3/19/92, from lipid methyl acetate +X CT3 CT3 X 0.1525 3 0.00 ! ALLOW ALI + ! alkane, 4/98, yin and mackerell +X CT3 NC2 X 0.0000 6 180.00 ! ALLOW ALI POL + ! methylguanidinium, adm jr., 3/26/92 +X CT3 NH2 X 0.1100 3 0.00 ! ALLOW POL + ! methylamine geom/freq, adm jr., 6/2/92 +X CT3 NH3 X 0.0900 3 0.00 ! ALLOW ALI POL + ! fine-tuned to ab initio; METHYLAMMONIUM, KK 03/10/92 +X CT3 OH1 X 0.1400 3 0.00 ! ALLOW ALI ALC ARO + ! EMB 11/21/89 methanol vib fit +X CT3 OS X -0.1000 3 0.00 ! ALLOW PEP POL + ! adm jr. 3/19/92, from lipid methyl acetate + +!chi1/chi2 fitting, Zhu, 2011 +!directly transferred parameters +NH1 CT1 CT1 HA1 0.2000 3 0.00 ! From X CT1 CT1 X +HB1 CT1 CT1 HA1 0.2000 3 0.00 ! From X CT1 CT1 X +HB1 CT1 CT1 CT3 0.2000 3 0.00 ! From X CT1 CT1 X +HA1 CT1 CT1 C 0.2000 3 0.00 ! From X CT1 CT1 X +! +NH1 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CT1 CT2 OH1 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CT1 CT2 CT2 0.2000 3 0.00 ! From X CT1 CT2 X +HA2 CT2 CT1 C 0.2000 3 0.00 ! From X CT1 CT2 X +HA2 CT2 OH1 H 0.1400 3 0.00 ! From X CT2 OH1 X +! +CT1 CT2 CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X +HA2 CT2 CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X +HA2 CT2 CT2 CC 0.1900 3 0.00 ! From X CT2 CT2 X +! +HB1 CT1 CT2 S 0.2000 3 0.00 ! From X CT1 CT2 X +!Arg +CT2 CT2 CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X +CT2 CT2 CT2 NC2 0.1900 3 0.00 ! From X CT2 CT2 X +CT2 CT2 NC2 HC 0.0000 6 180.00 ! From X CT2 NC2 X +CT2 CT2 NC2 C 0.0000 6 180.00 ! From X CT2 NC2 X +HA2 CT2 CT2 NC2 0.1900 3 0.00 ! From X CT2 CT2 X +CT2 NC2 C NC2 2.2500 2 180.00 ! From X C NC2 X +HA2 CT2 NC2 HC 0.0000 6 180.00 ! From X CT2 NC2 X +HA2 CT2 NC2 C 0.0000 6 180.00 ! From X CT2 NC2 X +NC2 C NC2 HC 2.2500 2 180.00 ! From X C NC2 X +!Asn +HB1 CT1 CT2 CC 0.2000 3 0.00 ! From X CT1 CT2 X +!Trp +HB1 CT1 CT2 CY 0.2000 3 0.00 ! From X CT1 CT2 X +!Asp +HA2 CT2 CC OC 0.0500 6 180.00 ! From X CT2 CC X +!Hsd/Hse +HB1 CT1 CT2 CPH1 0.2000 3 0.00 ! From X CT1 CT2 X +!Ile,Leu,Val +CT1 CT1 CT3 HA3 0.2000 3 0.00 ! From X CT1 CT3 X +CT1 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CT1 CT1 CT2 0.2000 3 0.00 ! From X CT1 CT1 X +CT1 CT2 CT3 HA3 0.1600 3 0.00 ! From X CT2 CT3 X +HA1 CT1 CT3 HA3 0.2000 3 0.00 ! From X CT1 CT3 X +HA1 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X +HA1 CT1 CT2 CT3 0.2000 3 0.00 ! From X CT1 CT2 X +CT3 CT1 CT2 HA2 0.2000 3 0.00 ! From X CT1 CT2 X +CT3 CT1 CT2 CT3 0.2000 3 0.00 ! From X CT1 CT2 X +HA3 CT3 CT1 CT2 0.2000 3 0.00 ! From X CT1 CT3 X +HA2 CT2 CT3 HA3 0.1600 3 0.00 ! From X CT2 CT3 X +CT1 CT2 CT1 HA1 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CT1 CT2 CT1 0.2000 3 0.00 ! From X CT1 CT2 X +CT3 CT1 CT3 HA3 0.2000 3 0.00 ! From X CT1 CT3 X +!Lys +CT2 CT2 CT2 NH3 0.1900 3 0.00 ! From X CT2 CT2 X +CT2 CT2 NH3 HC 0.1000 3 0.00 ! From X CT2 NH3 X +HA2 CT2 CT2 NH3 0.1900 3 0.00 ! From X CT2 CT2 X +HA2 CT2 NH3 HC 0.1000 3 0.00 ! From X CT2 NH3 X +!Tyr/Phe +HB1 CT1 CT2 CA 0.2000 3 0.00 ! From X CT1 CT2 X +HA2 CT2 CA CA 0.0000 6 0.00 ! From X CT2 CA X +!Thr +HB1 CT1 CT1 OH1 0.2000 3 0.00 ! From X CT1 CT1 X +HA1 CT1 OH1 H 0.1400 3 0.00 ! From X CT1 OH1 X +OH1 CT1 CT3 HA3 0.2000 3 0.00 ! From X CT1 CT3 X +!Gln +CT2 CT2 CC O 0.0500 6 180.00 ! From X CT2 CC X +CT2 CT2 CC NH2 0.0500 6 180.00 ! From X CT2 CC X +!Glu +CT2 CT2 CC OC 0.0500 6 180.00 ! From X CT2 CC X +!Glu/Hsp +NH1 CT1 CT2A HA2 0.2000 3 0.00 ! From X CT1 CT2 X +NH2 CT1 CT2A CT2 0.2000 3 0.00 ! From X CT1 CT2 X !N terminus +NH3 CT1 CT2A CT2 0.2000 3 0.00 ! From X CT1 CT2 X !N terminus +CT1 CT2A CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X +HB1 CT1 CT2A HA2 0.2000 3 0.00 ! From X CT1 CT2 X +HB1 CT1 CT2A CT2 0.2000 3 0.00 ! From X CT1 CT2 X +HA2 CT2A CT1 C 0.2000 3 0.00 ! From X CT1 CT2 X +HA2 CT2A CT1 CC 0.2000 3 0.00 ! RB: added for C-ter Glu +HA2 CT2A CT2 HA2 0.1900 3 0.00 ! From X CT2 CT2 X +HA2 CT2A CT2 CC 0.1900 3 0.00 ! From X CT2 CT2 X +HB1 CT1 CT2A CPH1 0.2000 3 0.00 ! From X CT1 CT2 X +C NH1 CT1 CT2A 1.8000 1 0.00 ! from CT2 CT1 NH1 C +H NH1 CT1 CT2A 0.0000 1 0.00 ! from H NH1 CT1 CT2 +CT2A CT1 C O 1.4000 1 0.00 ! from O C CT1 CT2 +CT2A CT1 C NH1 0.0000 1 0.00 ! NH1 C CT1 CT2 +CT2A CT1 C N 0.0000 1 0.00 ! RB: added for GLU-PRO in UBQ +! Glup +CT1 CT2A CT2 CD 0.1900 3 0.00 ! From X CT2 CT2 X +HA2 CT2A CT2 CD 0.1900 3 0.00 ! From X CT2 CT2 X +CT2A CPH1 CPH1 HR1 1.0000 2 180.00 ! from HR1 CPH1 CPH1 CT2 +CT2A CPH1 CPH1 NR3 2.5000 2 180.00 ! from NR3 CPH1 CPH1 CT2 +CT2A CPH1 NR3 H 3.0000 2 180.00 ! from H NR3 CPH1 CT2 +CT2A CPH1 NR3 CPH2 2.5000 2 180.00 ! from CT2 CPH1 NR3 CPH2 +HA2 CT2A CPH1 CPH1 0.0000 3 0.00 ! from HA2 CT2 CPH1 CPH1 +HA2 CT2A CPH1 NR3 0.1900 3 0.00 ! from NR3 CPH1 CT2 HA2 + +! Fit dihedrals +! Variable cutoff based on QM and weighted in favor of alphaR and EXT (5:5:1) +! Shared dihedrals were fitted simultaneously + +! Group-fitted for Lys/Arg/Gln/Met +C CT1 CT2 CT2 0.3500 1 180.00 +C CT1 CT2 CT2 0.4200 2 180.00 +C CT1 CT2 CT2 1.9100 3 180.00 +CT2 CT2 CT1 NH1 0.8800 1 180.00 +CT2 CT2 CT1 NH1 0.0000 2 180.00 +CT2 CT2 CT1 NH1 1.9000 3 0.00 +CC CT2 CT2 CT1 1.8400 1 180.00 +CC CT2 CT2 CT1 0.8400 2 180.00 +CC CT2 CT2 CT1 0.3900 3 180.00 +CT1 CT2 CT2 CT2 0.6300 1 180.00 +CT1 CT2 CT2 CT2 0.0100 2 0.00 +CT1 CT2 CT2 CT2 0.1500 3 0.00 +CT1 CT2 CT2 S 0.1400 1 180.00 +CT1 CT2 CT2 S 0.5400 2 0.00 +CT1 CT2 CT2 S 0.6900 3 0.00 +! Fitted Asn +C CT1 CT2 CC 1.4100 1 180.00 +C CT1 CT2 CC 1.2900 2 180.00 +C CT1 CT2 CC 0.5900 3 180.00 +CC CT2 CT1 NH1 0.2800 1 180.00 +CC CT2 CT1 NH1 0.5000 2 180.00 +CC CT2 CT1 NH1 0.3800 3 0.00 +CT1 CT2 CC NH2 0.6200 1 180.00 +CT1 CT2 CC NH2 0.6600 2 180.00 +CT1 CT2 CC NH2 0.7200 3 180.00 +CT1 CT2 CC O 0.4200 1 180.00 +CT1 CT2 CC O 0.1500 2 180.00 +CT1 CT2 CC O 0.9500 3 180.00 +! Fitted Asp +C CT1 CT2A CC 1.6100 1 180.00 +C CT1 CT2A CC 1.2900 2 180.00 +C CT1 CT2A CC 0.5900 3 180.00 +CC CT2A CT1 NH1 0.6800 1 180.00 +CC CT2A CT1 NH1 0.1000 2 180.00 +CC CT2A CT1 NH1 0.3800 3 0.00 +CT1 CT2A CC OC 0.8400 1 0.00 +CT1 CT2A CC OC 0.9800 2 180.00 +CT1 CT2A CC OC 1.4600 3 0.00 +! Fitted Cys +CT1 CT2 S HS 0.2000 1 0.00 +CT1 CT2 S HS 0.6500 2 0.00 +CT1 CT2 S HS 0.2200 3 0.00 +C CT1 CT2 S 0.2400 1 180.00 +C CT1 CT2 S 0.7500 2 180.00 +C CT1 CT2 S 1.3500 3 180.00 +NH1 CT1 CT2 S 0.3400 1 0.00 +NH1 CT1 CT2 S 0.5000 2 180.00 +NH1 CT1 CT2 S 1.4300 3 0.00 +! Fitted Glu +CC CT2 CT2A CT1 0.0000 1 180.00 +CC CT2 CT2A CT1 0.3800 2 180.00 +CC CT2 CT2A CT1 0.5900 3 180.00 +C CT1 CT2A CT2 0.1100 1 0.00 +C CT1 CT2A CT2 0.9800 2 180.00 +C CT1 CT2A CT2 1.6000 3 180.00 +CC CT1 CT2A CT2 1.6000 3 180.00 +CT2 CT2A CT1 NH1 0.3000 1 0.00 +CT2 CT2A CT1 NH1 0.3500 2 0.00 +CT2 CT2A CT1 NH1 1.7600 3 0.00 +! Group-fitted for Hsd/Hse +CPH1 CPH1 CT2 CT1 1.7400 1 0.00 +CPH1 CPH1 CT2 CT1 0.1500 2 0.00 +CPH1 CPH1 CT2 CT1 0.7700 3 180.00 +CT1 CT2 CPH1 NR1 1.4900 1 0.00 +CT1 CT2 CPH1 NR1 0.0900 2 180.00 +CT1 CT2 CPH1 NR1 0.7900 3 180.00 +CT1 CT2 CPH1 NR2 1.0900 1 0.00 +CT1 CT2 CPH1 NR2 0.0900 2 0.00 +CT1 CT2 CPH1 NR2 0.6700 3 180.00 +C CT1 CT2 CPH1 0.1800 1 180.00 +C CT1 CT2 CPH1 0.6400 2 180.00 +C CT1 CT2 CPH1 0.8700 3 180.00 +CPH1 CT2 CT1 NH1 0.0000 1 0.00 +CPH1 CT2 CT1 NH1 0.0000 2 180.00 +CPH1 CT2 CT1 NH1 0.9000 3 0.00 +! Fitted Hsp +CPH1 CPH1 CT2A CT1 2.0400 1 0.00 +CPH1 CPH1 CT2A CT1 0.4400 2 0.00 +CPH1 CPH1 CT2A CT1 0.1300 3 180.00 +CT1 CT2A CPH1 NR3 0.5300 1 180.00 +CT1 CT2A CPH1 NR3 0.4200 2 180.00 +CT1 CT2A CPH1 NR3 0.3000 3 180.00 +C CT1 CT2A CPH1 1.7500 1 180.00 +C CT1 CT2A CPH1 0.1300 2 0.00 +C CT1 CT2A CPH1 1.8600 3 180.00 +CPH1 CT2A CT1 NH1 1.0900 1 180.00 +CPH1 CT2A CT1 NH1 0.2200 2 180.00 +CPH1 CT2A CT1 NH1 2.3200 3 0.00 +! Group-fitted for Ile/Thr +CT1 CT1 CT2 CT3 0.3800 1 180.00 +CT1 CT1 CT2 CT3 0.1300 2 180.00 +CT1 CT1 CT2 CT3 0.2900 3 180.00 +C CT1 CT1 CT2 0.1000 1 180.00 +C CT1 CT1 CT2 0.5200 2 180.00 +C CT1 CT1 CT2 0.2900 3 180.00 +CT2 CT1 CT1 NH1 0.1200 1 180.00 +CT2 CT1 CT1 NH1 0.3600 2 180.00 +CT2 CT1 CT1 NH1 0.4100 3 0.00 +! Fitted Leu +CT1 CT2 CT1 CT3 0.0500 1 0.00 +CT1 CT2 CT1 CT3 0.1000 2 180.00 +CT1 CT2 CT1 CT3 0.0100 3 180.00 +C CT1 CT2 CT1 0.3200 1 180.00 +C CT1 CT2 CT1 0.6100 2 180.00 +C CT1 CT2 CT1 0.7200 3 180.00 +CT1 CT2 CT1 NH1 0.4800 1 180.00 +CT1 CT2 CT1 NH1 0.4200 2 180.00 +CT1 CT2 CT1 NH1 0.6500 3 0.00 +! Group-fitted for Phe/Tyr +CA CA CT2 CT1 1.0700 1 0.00 +CA CA CT2 CT1 0.2400 2 180.00 +CA CA CT2 CT1 0.1700 3 180.00 +C CT1 CT2 CA 1.2800 1 180.00 +C CT1 CT2 CA 0.9400 2 180.00 +C CT1 CT2 CA 1.5700 3 180.00 +CA CT2 CT1 NH1 0.5200 1 180.00 +CA CT2 CT1 NH1 0.6200 2 180.00 +CA CT2 CT1 NH1 1.5800 3 0.00 +! Fitted Ser +CT1 CT2 OH1 H 0.0200 1 0.00 +CT1 CT2 OH1 H 0.5600 2 0.00 +CT1 CT2 OH1 H 0.4900 3 0.00 +C CT1 CT2 OH1 0.6500 1 180.00 +C CT1 CT2 OH1 0.2500 2 180.00 +C CT1 CT2 OH1 1.1700 3 180.00 +NH1 CT1 CT2 OH1 0.1800 1 180.00 +NH1 CT1 CT2 OH1 0.1900 2 180.00 +NH1 CT1 CT2 OH1 1.4600 3 0.00 +! Group-fitted for Ile/Thr +CT1 CT1 OH1 H 0.1800 1 0.00 +CT1 CT1 OH1 H 0.0600 2 0.00 +CT1 CT1 OH1 H 0.2500 3 0.00 +C CT1 CT1 OH1 0.7900 1 180.00 +C CT1 CT1 OH1 0.3900 2 180.00 +C CT1 CT1 OH1 0.9900 3 180.00 +NH1 CT1 CT1 OH1 0.0900 1 0.00 +NH1 CT1 CT1 OH1 0.1900 2 180.00 +NH1 CT1 CT1 OH1 0.1700 3 0.00 +! Fitted Trp +CA CY CT2 CT1 0.0300 1 0.00 +CA CY CT2 CT1 0.5500 2 0.00 +CA CY CT2 CT1 0.3900 3 180.00 +CPT CY CT2 CT1 0.3600 1 180.00 +CPT CY CT2 CT1 0.0500 2 0.00 +CPT CY CT2 CT1 0.1900 3 180.00 +C CT1 CT2 CY 1.0900 1 180.00 +C CT1 CT2 CY 0.5000 2 180.00 +C CT1 CT2 CY 1.1700 3 180.00 +CY CT2 CT1 NH1 0.2900 1 180.00 +CY CT2 CT1 NH1 0.6600 2 180.00 +CY CT2 CT1 NH1 1.1700 3 0.00 +! Fitted Val +C CT1 CT1 CT3 0.1400 1 180.00 +C CT1 CT1 CT3 0.2600 2 180.00 +C CT1 CT1 CT3 0.3300 3 180.00 +CT3 CT1 CT1 NH1 0.1800 1 0.00 +CT3 CT1 CT1 NH1 0.0600 2 0.00 +CT3 CT1 CT1 NH1 0.5900 3 0.00 +!ASP, CT2->CT2A, jshim +H NH1 CT2A CC 0.0000 1 0.00 +X CT2A CC X 0.0500 6 180.00 +HB1 CT1 CT2A CC 0.2000 3 0.00 +HA2 CT2A CC OC 0.0500 6 180.00 +NH3 CT1 CT2A HA2 0.2000 3 0.00 +NH3 CT1 CT2A CC 0.2000 3 0.00 +CC CT2A CT1 CC 0.2000 3 0.00 +!termini specific terms +CPH1 CT2A CT1 CC 0.2000 3 0.00 +CPH1 CT2A CT1 NH3 0.2000 3 0.00 +CPH1 CT2A CT1 CD 0.2000 3 0.00 +HA2 CT2A CT1 CD 0.2000 3 0.00 +CT2 CT2A CT1 CD 0.2000 3 0.00 +! RESI CYSM and PRES CYSD +H NH2 CT1 CS 0.1100 3 0.00 ! from H NH2 CT1 CT2 or H NH2 CT1 CT2 , kevo +CS CT1 NH1 C 1.8000 1 0.00 ! from CT2 CT1 NH1 C or CT2A CT1 NH1 C , kevo +H NH1 CT1 CS 0.0000 1 0.00 ! from H NH1 CT1 CT2 or H NH1 CT1 CT2 , kevo +N C CT1 CS 0.0000 1 0.00 ! from N C CT1 CT2 or N C CT1 CT2 , kevo +NH1 C CT1 CS 0.0000 1 0.00 ! from NH1 C CT1 CT2 or NH1 C CT1 CT2 , kevo +O C CT1 CS 1.4000 1 0.00 ! from O C CT1 CT2 or O C CT1 CT2 , kevo +HA2 CS CT1 C 0.2000 3 0.00 ! from HA2 CT2 CT1 C or HA2 CT2A CT1 C , kevo +NH1 CT1 CS HA2 0.2000 3 0.00 ! from NH1 CT1 CT2 HA2 or NH1 CT1 CT2A HA2 , kevo +HB1 CT1 CS HA2 0.2000 3 0.00 ! from HB1 CT1 CT2 HA2 or HB1 CT1 CT2A HA2 , kevo +HB1 CT1 CS SS 0.2000 3 0.00 ! from HB1 CT1 CT2 S or HB1 CT1 CT2A S , kevo +C CT1 CS SS 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +NH1 CT1 CS SS 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +! Termini +NH3 CT1 CS HA2 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +NH3 CT1 CS SS 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +NH2 CT1 CS HA2 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +NH2 CT1 CS SS 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +CC CT1 CS HA2 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +CC CT1 CS SS 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +CD CT1 CS HA2 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +CD CT1 CS SS 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +! PRES SERD +NH1 CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +NH2 CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +NH3 CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +C CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +CC CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +CD CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo +HB1 CT1 CT2 OC 0.2000 3 0.00 ! from X CT1 CT2 X , kevo + +NONBONDED nbxmod 5 atom cdiel fshift vatom vdistance vfswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 2013 correction + +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +!Anisole /: Parameters from TraPPE 4 +!SPC/E Water +HT 0.000000 0.00000 0.00000 0.0 0.0 0.0 +OT 0.000000 -0.15541 1.7774185 0.0 0.0 0.0 + +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +!carbons +C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO + ! NMA pure solvent, adm jr., 3/3/93 +CA 0.000000 -0.070000 1.992400 ! ALLOW ARO + ! benzene (JES) +CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO + ! adm jr. 3/3/92, acetic acid heat of solvation +CD 0.000000 -0.070000 2.000000 ! ALLOW POL + ! adm jr. 3/19/92, acetate a.i. and dH of solvation +CE1 0.000000 -0.068000 2.090000 ! + ! for propene, yin/adm jr., 12/95 +CE2 0.000000 -0.064000 2.080000 ! + ! for ethene, yin/adm jr., 12/95 +CP1 0.000000 -0.020000 2.275000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP2 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CP3 0.000000 -0.055000 2.175000 0.000000 -0.010000 1.900000 ! ALLOW ALI + ! alkane update, adm jr., 3/2/92 +CPH1 0.000000 -0.050000 1.800000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CPH2 0.000000 -0.050000 1.800000 ! ALLOW ARO + ! adm jr., 10/23/91, imidazole solvation and sublimation +CS 0.000000 -0.110000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 +CPT 0.000000 -0.099000 1.860000 ! atm, indole vaporization 5/05 +CY 0.000000 -0.073000 1.990000 ! atm, indole vaporization 5/05 +CAI 0.000000 -0.073000 1.990000 ! atm, indole vaporization 5/05 + ! TRP, JWK 08/29/89 +!new alkanes atoms types for conversion to new LJ parameters for c27 +CT 0.0 -0.0200 2.275 0.0 -0.01 1.9 ! +CT1 0.0 -0.0320 2.000 0.0 -0.01 1.9 ! alkane, 4/07, viv and adm jr. +CT2 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. +CT2A 0.0 -0.0560 2.010 0.0 -0.01 1.9 ! from CT2 (GLU, HSP), 05282010, zhu +CT3 0.0 -0.0780 2.040 0.0 -0.01 1.9 ! alkane, 4/98, yin, adm jr. +! hydrogens +H 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC + ! same as TIP3P hydrogen, adm jr., 7/20/89 +HA 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HB1 0.000000 -0.022000 1.320000 ! + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HB2 0.000000 -0.028000 1.340000 ! + ! Yin and MacKerell, adm jr., 5/30/02 +HE1 0.000000 -0.031000 1.250000 ! + ! for propene, yin/adm jr., 12/95 +HE2 0.000000 -0.026000 1.260000 ! + ! for ethene, yin/adm jr., 12/95 +!HB 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC + ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92 +HC 0.000000 -0.046000 0.224500 ! ALLOW POL + ! new, small polar Hydrogen, see also adm jr. JG 8/27/89 +HP 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO + ! JES 8/25/89 values from Jorgensen fit to hydration energy +HR1 0.000000 -0.046000 0.900000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR2 0.000000 -0.046000 0.700000 ! ALLOW ARO + ! adm jr., 6/27/90, his +HR3 0.000000 -0.007800 1.468000 ! ALLOW ARO + ! adm jr., 3/24/92, maintain old aliphatic H VDW params +HS 0.000000 -0.100000 0.450000 ! ALLOW SUL + ! methanethiol pure solvent, adm jr., 6/22/92 +!new alkanes atoms types for conversion to new LJ parameters for c27 (see toppar_all22_prot_aliphatic_c27.str) +HA1 0.0 -0.045 1.3400 ! alkane, viv and adm jr., 4/07 +HA2 0.0 -0.034 1.3400 ! alkane, viv and adm jr., 4/07 +HA3 0.0 -0.024 1.3400 ! alkane, yin and mackerell, 4/98 +!nitrogens +N 0.000000 -0.200000 1.850000 0.000000 -0.000100 1.850000 ! ALLOW PRO + ! 6-31g* AcProNH2, ProNH2, 6-31g*//3-21g AcProNHCH3 RLD 4/23/93 +NC2 0.000000 -0.200000 1.850000 ! ALLOW POL + ! JG 8/27/89; note: NH1 in ARG was changed to NC2. +NH1 0.000000 -0.200000 1.850000 0.000000 -0.200000 1.550000 ! ALLOW PEP POL ARO + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +NH2 0.000000 -0.200000 1.850000 ! ALLOW POL + ! adm jr. +NH3 0.000000 -0.200000 1.850000 ! ALLOW POL + ! adm jr. +NP 0.000000 -0.200000 1.850000 ! ALLOW PRO + ! N-terminal proline; from 6-31g* +ProNH2 RLD 9/28/90 +NR1 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR2 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NR3 0.000000 -0.200000 1.850000 ! ALLOW ARO + ! His, adm jr., 9/4/89 +NY 0.000000 -0.200000 1.850000 ! atm, indole vaporization 5/05 +! oxygens +O 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL + ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK) +OB 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL ARO + ! adm jr., 10/17/90, acetic acid carbonyl O +OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION + ! JG 8/27/89 +OH1 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO + ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P) +OS 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO + ! adm jr. 9/17/90, avoid O* wildcard +! sulfurs +S 0.000000 -0.450000 2.000000 ! ALLOW SUL ION + ! adm jr., 3/3/92, methanethiol/ethylmethylsulfide pure solvent +SM 0.000000 -0.380000 1.975000 ! ALLOW SUL ION + ! adm jr., 3/3/92, dimethyldisulphide pure solvent +SS 0.000000 -0.470000 2.200000 ! ALLOW SUL + ! methylthiolate to water and F.E. of solvation, adm jr. 6/1/92 + +END diff --git a/test/input/PSFParser/BOX_0.pdb b/test/input/PSFParser/BOX_0.pdb new file mode 100644 index 000000000..567b82b91 --- /dev/null +++ b/test/input/PSFParser/BOX_0.pdb @@ -0,0 +1,54 @@ +CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 +ATOM 1 O1 SPCE0 1 6.785 39.521 0.350 1.00 0.00 0000 +ATOM 2 H1 SPCE0 1 6.965 39.459 1.333 1.00 0.00 0000 +ATOM 3 H2 SPCE0 1 5.961 40.066 0.195 1.00 0.00 0000 +ATOM 4 N ALA 0 2 16.108 21.301 19.992 1.00 0.00 0001 N +ATOM 5 HT1 ALA 0 2 16.807 21.988 19.795 0.00 0.00 0001 +ATOM 6 HT2 ALA 0 2 15.657 21.513 20.859 0.00 0.00 0001 +ATOM 7 HT3 ALA 0 2 15.434 21.279 19.254 0.00 0.00 0001 +ATOM 8 CA ALA 0 2 16.744 19.991 20.094 1.00 0.00 0001 C +ATOM 9 HA ALA 0 2 17.205 19.745 19.120 1.00 0.00 0001 H +ATOM 10 CB ALA 0 2 17.841 20.087 21.170 1.00 0.00 0001 C +ATOM 11 HB1 ALA 0 2 18.599 20.853 20.916 1.00 0.00 0001 H +ATOM 12 HB2 ALA 0 2 17.429 20.357 22.161 1.00 0.00 0001 H +ATOM 13 HB3 ALA 0 2 18.383 19.132 21.292 1.00 0.00 0001 H +ATOM 14 C ALA 0 2 15.725 18.918 20.392 1.00 0.00 0001 C +ATOM 15 O ALA 0 2 14.846 19.068 21.250 1.00 0.00 0001 O +ATOM 16 N ALA 0 3 15.773 17.810 19.734 1.00 0.00 0001 N +ATOM 17 HN ALA 0 3 16.439 17.584 19.024 0.00 0.00 0001 +ATOM 18 CA ALA 0 3 14.788 16.772 20.022 1.00 0.00 0001 C +ATOM 19 HA ALA 0 3 14.374 16.947 21.032 1.00 0.00 0001 H +ATOM 20 CB ALA 0 3 13.662 16.895 18.980 1.00 0.00 0001 C +ATOM 21 HB1 ALA 0 3 13.179 17.889 19.013 1.00 0.00 0001 H +ATOM 22 HB2 ALA 0 3 14.033 16.751 17.946 1.00 0.00 0001 H +ATOM 23 HB3 ALA 0 3 12.864 16.149 19.146 1.00 0.00 0001 H +ATOM 24 C ALA 0 3 15.429 15.405 20.030 1.00 0.00 0001 C +ATOM 25 OT1 ALA 0 3 16.405 15.502 19.834 0.00 0.00 0001 +ATOM 26 OT2 ALA 0 3 14.730 14.719 20.230 0.00 0.00 0001 +ATOM 27 N ALA 0 4 20.461 9.931 27.295 1.00 0.00 0002 N +ATOM 28 HT1 ALA 0 4 21.031 10.623 26.852 0.00 0.00 0002 +ATOM 29 HT2 ALA 0 4 20.491 9.079 26.773 0.00 0.00 0002 +ATOM 30 HT3 ALA 0 4 20.783 9.771 28.228 0.00 0.00 0002 +ATOM 31 CA ALA 0 4 19.083 10.411 27.344 1.00 0.00 0002 C +ATOM 32 HA ALA 0 4 19.051 11.331 27.957 1.00 0.00 0002 H +ATOM 33 CB ALA 0 4 18.652 10.741 25.904 1.00 0.00 0002 C +ATOM 34 HB1 ALA 0 4 19.302 11.512 25.447 1.00 0.00 0002 H +ATOM 35 HB2 ALA 0 4 18.692 9.853 25.244 1.00 0.00 0002 H +ATOM 36 HB3 ALA 0 4 17.619 11.131 25.862 1.00 0.00 0002 H +ATOM 37 C ALA 0 4 18.181 9.398 28.007 1.00 0.00 0002 C +ATOM 38 O ALA 0 4 18.235 8.193 27.734 1.00 0.00 0002 O +ATOM 39 N ALA 0 5 17.326 9.802 28.885 1.00 0.00 0002 N +ATOM 40 HN ALA 0 5 17.197 10.749 29.179 0.00 0.00 0002 +ATOM 41 CA ALA 0 5 16.454 8.822 29.526 1.00 0.00 0002 C +ATOM 42 HA ALA 0 5 16.400 7.923 28.885 1.00 0.00 0002 H +ATOM 43 CB ALA 0 5 17.086 8.449 30.878 1.00 0.00 0002 C +ATOM 44 HB1 ALA 0 5 18.099 8.024 30.755 1.00 0.00 0002 H +ATOM 45 HB2 ALA 0 5 17.184 9.326 31.549 1.00 0.00 0002 H +ATOM 46 HB3 ALA 0 5 16.487 7.693 31.418 1.00 0.00 0002 H +ATOM 47 C ALA 0 5 15.049 9.359 29.665 1.00 0.00 0002 C +ATOM 48 OT1 ALA 0 5 15.014 10.283 29.284 0.00 0.00 0002 +ATOM 49 OT2 ALA 0 5 14.478 8.667 30.106 0.00 0.00 0002 +ATOM 50 O1 SPCE0 6 13.795 39.569 0.364 1.00 0.00 0003 +ATOM 51 H1 SPCE0 6 13.629 38.602 0.169 1.00 0.00 0003 +ATOM 52 H2 SPCE0 6 12.929 40.021 0.577 1.00 0.00 0003 +END diff --git a/test/input/PSFParser/BOX_0.psf b/test/input/PSFParser/BOX_0.psf new file mode 100644 index 000000000..96243cd25 --- /dev/null +++ b/test/input/PSFParser/BOX_0.psf @@ -0,0 +1,177 @@ +PSF + + 1 !NTITLE + REMARKS VMD-generated NAMD/X-Plor PSF structure file + + 52 !NATOM + 1 0000 1 SPCE O1 OT -0.847600 15.9990 0 + 2 0000 1 SPCE H1 HT 0.423800 1.0080 0 + 3 0000 1 SPCE H2 HT 0.423800 1.0080 0 + 4 0001 2 ALA N NH3 -0.300000 14.0070 0 + 5 0001 2 ALA HT1 HC 0.330000 1.0080 0 + 6 0001 2 ALA HT2 HC 0.330000 1.0080 0 + 7 0001 2 ALA HT3 HC 0.330000 1.0080 0 + 8 0001 2 ALA CA CT1 0.210000 12.0110 0 + 9 0001 2 ALA HA HB1 0.100000 1.0080 0 + 10 0001 2 ALA CB CT3 -0.270000 12.0110 0 + 11 0001 2 ALA HB1 HA3 0.090000 1.0080 0 + 12 0001 2 ALA HB2 HA3 0.090000 1.0080 0 + 13 0001 2 ALA HB3 HA3 0.090000 1.0080 0 + 14 0001 2 ALA C C 0.510000 12.0110 0 + 15 0001 2 ALA O O -0.510000 15.9990 0 + 16 0001 3 ALA N NH1 -0.470000 14.0070 0 + 17 0001 3 ALA HN H 0.310000 1.0080 0 + 18 0001 3 ALA CA CT1 0.070000 12.0110 0 + 19 0001 3 ALA HA HB1 0.090000 1.0080 0 + 20 0001 3 ALA CB CT3 -0.270000 12.0110 0 + 21 0001 3 ALA HB1 HA3 0.090000 1.0080 0 + 22 0001 3 ALA HB2 HA3 0.090000 1.0080 0 + 23 0001 3 ALA HB3 HA3 0.090000 1.0080 0 + 24 0001 3 ALA C CC 0.340000 12.0110 0 + 25 0001 3 ALA OT1 OC -0.670000 15.9990 0 + 26 0001 3 ALA OT2 OC -0.670000 15.9990 0 + 27 0002 4 ALA N NH3 -0.300000 14.0070 0 + 28 0002 4 ALA HT1 HC 0.330000 1.0080 0 + 29 0002 4 ALA HT2 HC 0.330000 1.0080 0 + 30 0002 4 ALA HT3 HC 0.330000 1.0080 0 + 31 0002 4 ALA CA CT1 0.210000 12.0110 0 + 32 0002 4 ALA HA HB1 0.100000 1.0080 0 + 33 0002 4 ALA CB CT3 -0.270000 12.0110 0 + 34 0002 4 ALA HB1 HA3 0.090000 1.0080 0 + 35 0002 4 ALA HB2 HA3 0.090000 1.0080 0 + 36 0002 4 ALA HB3 HA3 0.090000 1.0080 0 + 37 0002 4 ALA C C 0.510000 12.0110 0 + 38 0002 4 ALA O O -0.510000 15.9990 0 + 39 0002 5 ALA N NH1 -0.470000 14.0070 0 + 40 0002 5 ALA HN H 0.310000 1.0080 0 + 41 0002 5 ALA CA CT1 0.070000 12.0110 0 + 42 0002 5 ALA HA HB1 0.090000 1.0080 0 + 43 0002 5 ALA CB CT3 -0.270000 12.0110 0 + 44 0002 5 ALA HB1 HA3 0.090000 1.0080 0 + 45 0002 5 ALA HB2 HA3 0.090000 1.0080 0 + 46 0002 5 ALA HB3 HA3 0.090000 1.0080 0 + 47 0002 5 ALA C CC 0.340000 12.0110 0 + 48 0002 5 ALA OT1 OC -0.670000 15.9990 0 + 49 0002 5 ALA OT2 OC -0.670000 15.9990 0 + 50 0003 6 SPCE O1 OT -0.847600 15.9990 0 + 51 0003 6 SPCE H1 HT 0.423800 1.0080 0 + 52 0003 6 SPCE H2 HT 0.423800 1.0080 0 + + 48 !NBOND: bonds + 1 2 1 3 4 8 4 5 + 4 6 4 7 8 9 8 10 + 8 14 10 11 10 12 10 13 + 14 16 14 15 16 17 16 18 + 18 19 18 20 18 24 20 21 + 20 22 20 23 24 26 24 25 + 27 31 27 28 27 29 27 30 + 31 32 31 33 31 37 33 34 + 33 35 33 36 37 39 37 38 + 39 40 39 41 41 42 41 43 + 41 47 43 44 43 45 43 46 + 47 49 47 48 50 51 50 52 + + 80 !NTHETA: angles + 2 1 3 4 8 9 4 8 14 + 5 4 8 5 4 7 5 4 6 + 6 4 8 6 4 7 7 4 8 + 8 14 15 8 14 16 8 10 13 + 8 10 12 8 10 11 9 8 10 + 10 8 14 4 8 10 11 10 13 + 11 10 12 12 10 13 9 8 14 + 16 18 19 16 18 24 15 14 16 + 14 16 17 17 16 18 18 20 23 + 18 20 22 18 20 21 14 16 18 + 19 18 20 20 18 24 16 18 20 + 21 20 23 21 20 22 22 20 23 + 19 18 24 18 24 25 18 24 26 + 25 24 26 27 31 32 27 31 37 + 28 27 31 28 27 30 28 27 29 + 29 27 31 29 27 30 30 27 31 + 31 37 38 31 37 39 31 33 36 + 31 33 35 31 33 34 32 31 33 + 33 31 37 27 31 33 34 33 36 + 34 33 35 35 33 36 32 31 37 + 39 41 42 39 41 47 38 37 39 + 37 39 40 40 39 41 41 43 46 + 41 43 45 41 43 44 37 39 41 + 42 41 43 43 41 47 39 41 43 + 44 43 46 44 43 45 45 43 46 + 42 41 47 41 47 48 41 47 49 + 48 47 49 51 50 52 + + 98 !NPHI: dihedrals + 4 8 10 11 4 8 10 12 + 4 8 10 13 4 8 14 16 + 4 8 14 15 5 4 8 10 + 5 4 8 14 5 4 8 9 + 6 4 8 10 6 4 8 14 + 6 4 8 9 7 4 8 10 + 7 4 8 14 7 4 8 9 + 8 14 16 17 8 14 16 18 + 9 8 10 11 9 8 10 12 + 9 8 10 13 9 8 14 16 + 9 8 14 15 10 8 14 16 + 10 8 14 15 14 8 10 11 + 14 8 10 12 14 8 10 13 + 14 16 18 20 14 16 18 24 + 14 16 18 19 15 14 16 17 + 15 14 16 18 16 18 20 21 + 16 18 20 22 16 18 20 23 + 16 18 24 26 16 18 24 25 + 17 16 18 20 17 16 18 24 + 17 16 18 19 19 18 20 21 + 19 18 20 22 19 18 20 23 + 19 18 24 26 19 18 24 25 + 20 18 24 26 20 18 24 25 + 24 18 20 21 24 18 20 22 + 24 18 20 23 27 31 33 34 + 27 31 33 35 27 31 33 36 + 27 31 37 39 27 31 37 38 + 28 27 31 33 28 27 31 37 + 28 27 31 32 29 27 31 33 + 29 27 31 37 29 27 31 32 + 30 27 31 33 30 27 31 37 + 30 27 31 32 31 37 39 40 + 31 37 39 41 32 31 33 34 + 32 31 33 35 32 31 33 36 + 32 31 37 39 32 31 37 38 + 33 31 37 39 33 31 37 38 + 37 31 33 34 37 31 33 35 + 37 31 33 36 37 39 41 43 + 37 39 41 47 37 39 41 42 + 38 37 39 40 38 37 39 41 + 39 41 43 44 39 41 43 45 + 39 41 43 46 39 41 47 49 + 39 41 47 48 40 39 41 43 + 40 39 41 47 40 39 41 42 + 42 41 43 44 42 41 43 45 + 42 41 43 46 42 41 47 49 + 42 41 47 48 43 41 47 49 + 43 41 47 48 47 41 43 44 + 47 41 43 45 47 41 43 46 + + 6 !NIMPHI: impropers + 14 8 16 15 16 14 18 17 + 24 18 26 25 37 31 39 38 + 39 37 41 40 47 41 49 48 + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 0 0 0 0 + 0 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/test/input/PSFParser/BOX_1.pdb b/test/input/PSFParser/BOX_1.pdb new file mode 100644 index 000000000..f77d7a0a5 --- /dev/null +++ b/test/input/PSFParser/BOX_1.pdb @@ -0,0 +1,8 @@ +CRYST1 0.000 0.000 0.000 90.00 90.00 90.00 P 1 1 +ATOM 1 O1 SPCE0 1 116.414 133.136 60.022 1.00 0.00 0000 +ATOM 2 H1 SPCE0 1 115.771 133.502 59.348 1.00 0.00 0000 +ATOM 3 H2 SPCE0 1 116.972 133.880 60.390 1.00 0.00 0000 +ATOM 4 O1 SPCE0 2 32.048 134.183 25.320 1.00 0.00 0001 +ATOM 5 H1 SPCE0 2 32.819 133.882 25.883 1.00 0.00 0001 +ATOM 6 H2 SPCE0 2 31.318 134.525 25.911 1.00 0.00 0001 +END diff --git a/test/input/PSFParser/BOX_1.psf b/test/input/PSFParser/BOX_1.psf new file mode 100644 index 000000000..ad2cd001d --- /dev/null +++ b/test/input/PSFParser/BOX_1.psf @@ -0,0 +1,38 @@ +PSF + + 1 !NTITLE + REMARKS VMD-generated NAMD/X-Plor PSF structure file + + 6 !NATOM + 1 0000 1 SPCE O1 OT -0.847600 15.9990 0 + 2 0000 1 SPCE H1 HT 0.423800 1.0080 0 + 3 0000 1 SPCE H2 HT 0.423800 1.0080 0 + 4 0001 2 SPCE O1 OT -0.847600 15.9990 0 + 5 0001 2 SPCE H1 HT 0.423800 1.0080 0 + 6 0001 2 SPCE H2 HT 0.423800 1.0080 0 + + 4 !NBOND: bonds + 1 2 1 3 4 5 4 6 + + 2 !NTHETA: angles + 2 1 3 5 4 6 + + 0 !NPHI: dihedrals + + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 0 0 0 0 0 0 + + 1 0 !NGRP + 0 0 0 + diff --git a/test/input/PSFParser/GRAPHENE_PORE_0.pdb b/test/input/PSFParser/GRAPHENE_PORE_0.pdb new file mode 100644 index 000000000..53569ba09 --- /dev/null +++ b/test/input/PSFParser/GRAPHENE_PORE_0.pdb @@ -0,0 +1,22 @@ +CRYST1 29.472 29.777 85.000 90.00 90.00 90.00 P 1 +ATOM 1 C1 TOP 1 1 -14.122 -14.180 27.500 1.00 1.00 C +ATOM 2 C2 TOP 1 1 14.122 -12.053 27.500 1.00 1.00 C +ATOM 3 C3 TOP 1 1 12.894 -9.926 27.500 1.00 1.00 C +ATOM 4 C4 TOP 1 1 11.666 -7.799 27.500 1.00 1.00 C +ATOM 5 C5 TOP 1 1 10.438 -5.672 27.500 1.00 1.00 C +ATOM 6 C6 TOP 1 1 9.210 -3.545 27.500 1.00 1.00 C +ATOM 7 C7 TOP 1 1 7.982 -1.418 27.500 1.00 1.00 C +ATOM 8 C8 TOP 1 1 6.754 0.709 27.500 1.00 1.00 C +ATOM 9 C9 TOP 1 1 5.526 2.836 27.500 1.00 1.00 C +ATOM 10 CA TOP 1 1 4.298 4.963 27.500 1.00 1.00 C +ATOM 11 C1 BOT 1 2 -14.122 -14.180 -0.500 1.00 1.00 C +ATOM 12 C2 BOT 1 2 14.122 -12.053 -0.500 1.00 1.00 C +ATOM 13 C3 BOT 1 2 12.894 -9.926 -0.500 1.00 1.00 C +ATOM 14 C4 BOT 1 2 11.666 -7.799 -0.500 1.00 1.00 C +ATOM 15 C5 BOT 1 2 10.438 -5.672 -0.500 1.00 1.00 C +ATOM 16 C6 BOT 1 2 9.210 -3.545 -0.500 1.00 1.00 C +ATOM 17 C7 BOT 1 2 7.982 -1.418 -0.500 1.00 1.00 C +ATOM 18 C8 BOT 1 2 6.754 0.709 -0.500 1.00 1.00 C +ATOM 19 C9 BOT 1 2 5.526 2.836 -0.500 1.00 1.00 C +ATOM 20 CA BOT 1 2 4.298 4.963 -0.500 1.00 1.00 C +END diff --git a/test/input/PSFParser/GRAPHENE_PORE_0.psf b/test/input/PSFParser/GRAPHENE_PORE_0.psf new file mode 100644 index 000000000..136431e51 --- /dev/null +++ b/test/input/PSFParser/GRAPHENE_PORE_0.psf @@ -0,0 +1,50 @@ +PSF + + 3 !NTITLE + REMARKS this file pore_3x3x2.8nm_1-layer - created by mBuild/foyer using the + REMARKS parameters from the {'H2O': 'files/mosdef_slitpore/ffxml/pore-spce.xml', 'BOT': 'files/mosdef_slitpore/ffxml/pore-spce.xml', 'TOP': 'files/mosdef_slitpore/ffxml/pore-spce.xml'} force field via MoSDef + REMARKS created on 2020-12-28 00:06:16.084336 + + + 20 !NATOM + 1 SYS 1 TOP C1 B 0.000000 12.0108 + 2 SYS 1 TOP C2 B 0.000000 12.0108 + 3 SYS 1 TOP C3 B 0.000000 12.0108 + 4 SYS 1 TOP C4 B 0.000000 12.0108 + 5 SYS 1 TOP C5 B 0.000000 12.0108 + 6 SYS 1 TOP C6 B 0.000000 12.0108 + 7 SYS 1 TOP C7 B 0.000000 12.0108 + 8 SYS 1 TOP C8 B 0.000000 12.0108 + 9 SYS 1 TOP C9 B 0.000000 12.0108 + 10 SYS 1 TOP CA B 0.000000 12.0108 + 11 SYS 2 BOT C1 A 0.000000 12.0108 + 12 SYS 2 BOT C2 A 0.000000 12.0108 + 13 SYS 2 BOT C3 A 0.000000 12.0108 + 14 SYS 2 BOT C4 A 0.000000 12.0108 + 15 SYS 2 BOT C5 A 0.000000 12.0108 + 16 SYS 2 BOT C6 A 0.000000 12.0108 + 17 SYS 2 BOT C7 A 0.000000 12.0108 + 18 SYS 2 BOT C8 A 0.000000 12.0108 + 19 SYS 2 BOT C9 A 0.000000 12.0108 + 20 SYS 2 BOT CA A 0.000000 12.0108 + + 0 !NBOND: bonds + + 0 !NTHETA: angles + + 0 !NPHI: dihedrals + + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 1 0 !NGRP + 0 0 0 diff --git a/test/input/PSFParser/GRAPHENE_PORE_1.pdb b/test/input/PSFParser/GRAPHENE_PORE_1.pdb new file mode 100644 index 000000000..53569ba09 --- /dev/null +++ b/test/input/PSFParser/GRAPHENE_PORE_1.pdb @@ -0,0 +1,22 @@ +CRYST1 29.472 29.777 85.000 90.00 90.00 90.00 P 1 +ATOM 1 C1 TOP 1 1 -14.122 -14.180 27.500 1.00 1.00 C +ATOM 2 C2 TOP 1 1 14.122 -12.053 27.500 1.00 1.00 C +ATOM 3 C3 TOP 1 1 12.894 -9.926 27.500 1.00 1.00 C +ATOM 4 C4 TOP 1 1 11.666 -7.799 27.500 1.00 1.00 C +ATOM 5 C5 TOP 1 1 10.438 -5.672 27.500 1.00 1.00 C +ATOM 6 C6 TOP 1 1 9.210 -3.545 27.500 1.00 1.00 C +ATOM 7 C7 TOP 1 1 7.982 -1.418 27.500 1.00 1.00 C +ATOM 8 C8 TOP 1 1 6.754 0.709 27.500 1.00 1.00 C +ATOM 9 C9 TOP 1 1 5.526 2.836 27.500 1.00 1.00 C +ATOM 10 CA TOP 1 1 4.298 4.963 27.500 1.00 1.00 C +ATOM 11 C1 BOT 1 2 -14.122 -14.180 -0.500 1.00 1.00 C +ATOM 12 C2 BOT 1 2 14.122 -12.053 -0.500 1.00 1.00 C +ATOM 13 C3 BOT 1 2 12.894 -9.926 -0.500 1.00 1.00 C +ATOM 14 C4 BOT 1 2 11.666 -7.799 -0.500 1.00 1.00 C +ATOM 15 C5 BOT 1 2 10.438 -5.672 -0.500 1.00 1.00 C +ATOM 16 C6 BOT 1 2 9.210 -3.545 -0.500 1.00 1.00 C +ATOM 17 C7 BOT 1 2 7.982 -1.418 -0.500 1.00 1.00 C +ATOM 18 C8 BOT 1 2 6.754 0.709 -0.500 1.00 1.00 C +ATOM 19 C9 BOT 1 2 5.526 2.836 -0.500 1.00 1.00 C +ATOM 20 CA BOT 1 2 4.298 4.963 -0.500 1.00 1.00 C +END diff --git a/test/input/PSFParser/GRAPHENE_PORE_1.psf b/test/input/PSFParser/GRAPHENE_PORE_1.psf new file mode 100644 index 000000000..4650e9d86 --- /dev/null +++ b/test/input/PSFParser/GRAPHENE_PORE_1.psf @@ -0,0 +1,51 @@ +PSF + + 3 !NTITLE + REMARKS this file pore_3x3x2.8nm_1-layer - created by mBuild/foyer using the + REMARKS parameters from the {'H2O': 'files/mosdef_slitpore/ffxml/pore-spce.xml', 'BOT': 'files/mosdef_slitpore/ffxml/pore-spce.xml', 'TOP': 'files/mosdef_slitpore/ffxml/pore-spce.xml'} force field via MoSDef + REMARKS created on 2020-12-28 00:06:16.084336 + + + 20 !NATOM + 1 SYS 1 TOP C1 B 0.000000 12.0108 + 2 SYS 1 TOP C2 B 0.000000 12.0108 + 3 SYS 1 TOP C3 B 0.000000 12.0108 + 4 SYS 1 TOP C4 B 0.000000 12.0108 + 5 SYS 1 TOP C5 B 0.000000 12.0108 + 6 SYS 1 TOP C6 B 0.000000 12.0108 + 7 SYS 1 TOP C7 B 0.000000 12.0108 + 8 SYS 1 TOP C8 B 0.000000 12.0108 + 9 SYS 1 TOP C9 B 0.000000 12.0108 + 10 SYS 1 TOP CA B 0.000000 12.0108 + 11 SYS 2 BOT C1 A 0.000000 12.0108 + 12 SYS 2 BOT C2 A 0.000000 12.0108 + 13 SYS 2 BOT C3 A 0.000000 12.0108 + 14 SYS 2 BOT C4 A 0.000000 12.0108 + 15 SYS 2 BOT C5 A 0.000000 12.0108 + 16 SYS 2 BOT C6 A 0.000000 12.0108 + 17 SYS 2 BOT C7 A 0.000000 12.0108 + 18 SYS 2 BOT C8 A 0.000000 12.0108 + 19 SYS 2 BOT C9 A 0.000000 12.0108 + 20 SYS 2 BOT CA A 0.000000 12.0108 + + 0 !NBOND: bonds + + 0 !NTHETA: angles + + 0 !NPHI: dihedrals + + + 0 !NIMPHI: impropers + + + 0 !NDON: donors + + + 0 !NACC: acceptors + + + 0 !NNB + + 1 0 !NGRP + 0 0 0 + diff --git a/test/input/water.par b/test/input/water.par new file mode 100644 index 000000000..36758cbdd --- /dev/null +++ b/test/input/water.par @@ -0,0 +1,58 @@ +*Parameter file for 1-octanol TraPPE-UA +*Parameters from TraPPE 5 +!*7/5/07 Added parameteres for SPC/E +!*7/8/07 Added parameters for nitromethane +!*7/12/07 Added parameteres for nitroethane +!*6/15/2012 includes refitted dihedral for alkanes/alcohols +! 8/6/2012 adding parameters for NTO +! 11/21/2012 MOST UP TO DATE +BONDS +! +!V(bond) = Kb(b - b0)**2 +! +!Kb: kcal/mole/A**2 +!b0: A +! +!atom type Kb b0 All constants from Charmm +OT HT 99999999999 1.0000 ! SPC bond length + + +ANGLES +! +!V(angle) = Ktheta(Theta - Theta0)**2 +! +!Kub: kcal/mole/A**2 (Urey-Bradley) +!S0: A +! +!atom types Ktheta Theta0 Kub S0 +! +HT OT HT 99999999999 109.5 0.0 0.0 ! water + + +DIHEDRALS +! +!V(dihedral) = Kchi(1 + cos(n(chi) - delta)) +! +!Kchi: kcal/mole +!n: multiplicity +!delta: degrees +! +!atom types Kchi n delta +! + +NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch - +cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5 + !adm jr., 5/08/91, suggested cutoff scheme +! +!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6] +! +!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j) +!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j +! +!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4 +! +!Anisole /: Parameters from TraPPE 4 +!SPC/E Water +HT 0.000000 0.00000 0.00000 0.0 0.0 0.0 +OT 0.000000 -0.15541 1.7774185 0.0 0.0 0.0 + diff --git a/test/src/CPUSideOutputTest.cpp b/test/src/CPUSideOutputTest.cpp new file mode 100644 index 000000000..cef3e6fa2 --- /dev/null +++ b/test/src/CPUSideOutputTest.cpp @@ -0,0 +1,14 @@ +#include +#include "CPUSide.h" +#include "Simulation.h" + +TEST(CPUSideOutput, CheckForConsistencyPDB_PSF_DCD) { + + std::string inputFileString = "outputTest.conf"; + Simulation sim(inputFileString.c_str()); + + CPUSide * cpu; + + + +} diff --git a/test/src/PSFParserTest.cpp b/test/src/PSFParserTest.cpp new file mode 100644 index 000000000..bfdf75d5d --- /dev/null +++ b/test/src/PSFParserTest.cpp @@ -0,0 +1,288 @@ +#include +#include "PDBSetup.h" +#include "PDBSetup.cpp" +#include "MolSetup.h" +#include "MolSetup.cpp" +#include "BondAdjacencyList.h" +#include "BondAdjacencyList.cpp" +#include "ConfigSetup.h" +#include "FFSetup.h" //For geometry kinds +#include "FFSetup.cpp" //For geometry kinds +#include "FFConst.h" +#include "FFConst.cpp" +#include "Reader.h" +#include "Reader.cpp" + + +TEST(PSFParserTest, CheckGraphenePoreTest) { + + config_setup::RestartSettings rs; + std::string pdbnames[2]; + + pdbnames[0] = "./test/input/PSFParser/GRAPHENE_PORE_0.pdb"; + pdbnames[1] = "./test/input/PSFParser/GRAPHENE_PORE_1.pdb"; + + PDBSetup pdb; + + pdb.Init(rs, pdbnames); + + std::string psfnames[2]; + bool psfdefined[2]; + + MolSetup ms; + + /* + Let GOMC parse dialanine + */ + + psfnames[0] = "./test/input/PSFParser/GRAPHENE_PORE_0.psf"; + psfnames[1] = "./test/input/PSFParser/GRAPHENE_PORE_1.psf"; + + psfdefined[0] = true; + psfdefined[1] = true; + + ms.Init(rs, psfnames, psfdefined, pdb.atoms); + + /* + Build the 10 atoms of TOP Sheet + */ + + std::vector TOP; + + mol_setup::Atom TOP_atom_1 = mol_setup::Atom( "C1", "TOP", 1, "SYS", "B", 0.000000, 12.0108); + mol_setup::Atom TOP_atom_2 = mol_setup::Atom( "C2", "TOP", 1, "SYS", "B", 0.000000, 12.0108); + mol_setup::Atom TOP_atom_3 = mol_setup::Atom( "C3", "TOP", 1, "SYS", "B", 0.000000, 12.0108); + mol_setup::Atom TOP_atom_4 = mol_setup::Atom( "C4", "TOP", 1, "SYS", "B", 0.000000, 12.0108); + mol_setup::Atom TOP_atom_5 = mol_setup::Atom( "C5", "TOP", 1, "SYS", "B", 0.000000, 12.0108); + mol_setup::Atom TOP_atom_6 = mol_setup::Atom( "C6", "TOP", 1, "SYS", "B", 0.000000, 12.0108); + mol_setup::Atom TOP_atom_7 = mol_setup::Atom( "C7", "TOP", 1, "SYS", "B", 0.000000, 12.0108); + mol_setup::Atom TOP_atom_8 = mol_setup::Atom( "C8", "TOP", 1, "SYS", "B", 0.000000, 12.0108); + mol_setup::Atom TOP_atom_9 = mol_setup::Atom( "C9", "TOP", 1, "SYS", "B", 0.000000, 12.0108); + mol_setup::Atom TOP_atom_10 = mol_setup::Atom( "CA", "TOP", 1, "SYS", "B", 0.000000, 12.0108); + + TOP.push_back(TOP_atom_1); + TOP.push_back(TOP_atom_2); + TOP.push_back(TOP_atom_3); + TOP.push_back(TOP_atom_4); + TOP.push_back(TOP_atom_5); + TOP.push_back(TOP_atom_6); + TOP.push_back(TOP_atom_7); + TOP.push_back(TOP_atom_8); + TOP.push_back(TOP_atom_9); + TOP.push_back(TOP_atom_10); + +/* + HB2 + | + HB1---CB---HB3 O + | | | + | | | HT1 + OT2``` | | | HA | + `` `.CA-.` `. C.` | N --HT2 + .- C : | `` N.` .` `.CA.- | + | | HA | | HT3 + | | HN | + | | | + OT1 HB1---CB---HB3 + | + HB2 +*/ + + + /* + Build the 10 atoms of TOP Sheet + */ + + std::vector BOT; + + mol_setup::Atom BOT_atom_1 = mol_setup::Atom( "C1", "BOT", 2, "SYS", "A", 0.000000, 12.0108); + mol_setup::Atom BOT_atom_2 = mol_setup::Atom( "C2", "BOT", 2, "SYS", "A", 0.000000, 12.0108); + mol_setup::Atom BOT_atom_3 = mol_setup::Atom( "C3", "BOT", 2, "SYS", "A", 0.000000, 12.0108); + mol_setup::Atom BOT_atom_4 = mol_setup::Atom( "C4", "BOT", 2, "SYS", "A", 0.000000, 12.0108); + mol_setup::Atom BOT_atom_5 = mol_setup::Atom( "C5", "BOT", 2, "SYS", "A", 0.000000, 12.0108); + mol_setup::Atom BOT_atom_6 = mol_setup::Atom( "C6", "BOT", 2, "SYS", "A", 0.000000, 12.0108); + mol_setup::Atom BOT_atom_7 = mol_setup::Atom( "C7", "BOT", 2, "SYS", "A", 0.000000, 12.0108); + mol_setup::Atom BOT_atom_8 = mol_setup::Atom( "C8", "BOT", 2, "SYS", "A", 0.000000, 12.0108); + mol_setup::Atom BOT_atom_9 = mol_setup::Atom( "C9", "BOT", 2, "SYS", "A", 0.000000, 12.0108); + mol_setup::Atom BOT_atom_10 = mol_setup::Atom( "CA", "BOT", 2, "SYS", "A", 0.000000, 12.0108); + + BOT.push_back(BOT_atom_1); + BOT.push_back(BOT_atom_2); + BOT.push_back(BOT_atom_3); + BOT.push_back(BOT_atom_4); + BOT.push_back(BOT_atom_5); + BOT.push_back(BOT_atom_6); + BOT.push_back(BOT_atom_7); + BOT.push_back(BOT_atom_8); + BOT.push_back(BOT_atom_9); + BOT.push_back(BOT_atom_10); + /* Compare GOMC Parser's TOP and BOT vs our Manual TOP and BOTs */ + + typedef std::vector::const_iterator atomIterator; + std::pair itPair1(ms.kindMap["BOT"].atoms.cbegin(), BOT.cbegin()); + for (; itPair1.second != BOT.cend(); ++itPair1.first, ++itPair1.second){ + EXPECT_EQ(*itPair1.first == *itPair1.second, true); + if (*itPair1.first == *itPair1.second){ + + } else { + std::cout << (*itPair1.first).name << " " << (*itPair1.first).mass << " not equal to " << (*itPair1.second).name << " " << (*itPair1.second).mass << std::endl; + } + } + + std::pair itPair2(ms.kindMap["TOP"].atoms.cbegin(), TOP.cbegin()); + for (; itPair2.second != TOP.cend(); ++itPair2.first, ++itPair2.second){ + EXPECT_EQ(*itPair2.first == *itPair2.second, true); + if (*itPair2.first == *itPair2.second){ + + } else { + std::cout << (*itPair2.first).name << " " << (*itPair2.first).mass << " not equal to " << (*itPair2.second).name << " " << (*itPair2.second).mass << std::endl; + } + } + +} + +TEST(PSFParserTest, CheckProtAndWaterTest) { + + config_setup::RestartSettings rs; + std::string pdbnames[2]; + + pdbnames[0] = "./test/input/PSFParser/BOX_0.pdb"; + pdbnames[1] = "./test/input/PSFParser/BOX_1.pdb"; + + PDBSetup pdb; + + pdb.Init(rs, pdbnames); + + std::string psfnames[2]; + bool psfdefined[2]; + + MolSetup ms; + + /* + Let GOMC parse dialanine + */ + + psfnames[0] = "./test/input/PSFParser/BOX_0.psf"; + psfnames[1] = "./test/input/PSFParser/BOX_1.psf"; + + psfdefined[0] = true; + psfdefined[1] = true; + + ms.Init(rs, psfnames, psfdefined, pdb.atoms); + + /* + Build the 3 atoms of SPCE + */ + + std::vector SPCE; + + mol_setup::Atom SPCE_1_atom_1 = mol_setup::Atom( "O1", "SPCE", 1, "0000", "OT", -0.847600, 15.9990); + mol_setup::Atom SPCE_1_atom_2 = mol_setup::Atom( "H1", "SPCE", 1, "0000", "HT", 0.423800, 1.0080); + mol_setup::Atom SPCE_1_atom_3 = mol_setup::Atom( "H2", "SPCE", 1, "0000", "HT", 0.423800, 1.0080); + + SPCE.push_back(SPCE_1_atom_1); + SPCE.push_back(SPCE_1_atom_2); + SPCE.push_back(SPCE_1_atom_3); + + +/* + HB2 + | + HB1---CB---HB3 O + | | | + | | | HT1 + OT2``` | | | HA | + `` `.CA-.` `. C.` | N --HT2 + .- C : | `` N.` .` `.CA.- | + | | HA | | HT3 + | | HN | + | | | + OT1 HB1---CB---HB3 + | + HB2 +*/ + + + /* + Manually Build the 23 atoms of dialanine + */ + /* PSF Col 4 3 2 1 5 6 7 */ + + std::vector DIALA; + + mol_setup::Atom DIALA_atom_1 = mol_setup::Atom( "N", "ALA", 2, "0003", "NH3", -0.300000, 14.0070); + mol_setup::Atom DIALA_atom_2 = mol_setup::Atom( "HT1", "ALA", 2, "0003", "HC", 0.330000, 1.0080); + mol_setup::Atom DIALA_atom_3 = mol_setup::Atom( "HT2", "ALA", 2, "0003", "HC", 0.330000, 1.0080); + mol_setup::Atom DIALA_atom_4 = mol_setup::Atom( "HT3", "ALA", 2, "0003", "HC", 0.330000, 1.0080); + mol_setup::Atom DIALA_atom_5 = mol_setup::Atom( "CA", "ALA", 2, "0003", "CT1", 0.210000, 12.0110); + mol_setup::Atom DIALA_atom_6 = mol_setup::Atom( "HA", "ALA", 2, "0003", "HB1", 0.100000, 1.0080); + mol_setup::Atom DIALA_atom_7 = mol_setup::Atom( "CB", "ALA", 2, "0003", "CT3", -0.270000, 12.0110); + mol_setup::Atom DIALA_atom_8 = mol_setup::Atom( "HB1", "ALA", 2, "0003", "HA3", 0.090000, 1.0080); + mol_setup::Atom DIALA_atom_9 = mol_setup::Atom( "HB2", "ALA", 2, "0003", "HA3", 0.090000, 1.0080); + mol_setup::Atom DIALA_atom_10 = mol_setup::Atom( "HB3", "ALA",2, "0003", "HA3", 0.090000, 1.0080); + mol_setup::Atom DIALA_atom_11 = mol_setup::Atom("C", "ALA", 2, "0003", "C", 0.510000, 12.0110); + mol_setup::Atom DIALA_atom_12 = mol_setup::Atom("O", "ALA", 2, "0003", "O", -0.510000, 15.9990); + mol_setup::Atom DIALA_atom_13 = mol_setup::Atom("N", "ALA", 3, "0003", "NH1", -0.470000, 14.0070); + mol_setup::Atom DIALA_atom_14 = mol_setup::Atom("HN", "ALA", 3, "0003", "H", 0.310000, 1.0080); + mol_setup::Atom DIALA_atom_15 = mol_setup::Atom("CA", "ALA", 3, "0003", "CT1", 0.070000, 12.0110); + mol_setup::Atom DIALA_atom_16 = mol_setup::Atom("HA", "ALA", 3, "0003", "HB1", 0.090000, 1.0080); + mol_setup::Atom DIALA_atom_17 = mol_setup::Atom("CB", "ALA", 3, "0003", "CT3", -0.270000, 12.0110); + mol_setup::Atom DIALA_atom_18 = mol_setup::Atom("HB1", "ALA", 3, "0003", "HA3", 0.090000, 1.0080); + mol_setup::Atom DIALA_atom_19 = mol_setup::Atom("HB2", "ALA", 3, "0003", "HA3", 0.090000, 1.0080); + mol_setup::Atom DIALA_atom_20 = mol_setup::Atom("HB3", "ALA", 3, "0003", "HA3", 0.090000, 1.0080); + mol_setup::Atom DIALA_atom_21 = mol_setup::Atom("C", "ALA", 3, "0003", "CC", 0.340000, 12.0110); + mol_setup::Atom DIALA_atom_22 = mol_setup::Atom("OT1", "ALA", 3, "0003", "OC", -0.670000, 15.9990); + mol_setup::Atom DIALA_atom_23 = mol_setup::Atom("OT2", "ALA", 3, "0003", "OC", -0.670000, 15.9990); + + DIALA.push_back(DIALA_atom_1); + DIALA.push_back(DIALA_atom_2); + DIALA.push_back(DIALA_atom_3); + DIALA.push_back(DIALA_atom_4); + DIALA.push_back(DIALA_atom_5); + DIALA.push_back(DIALA_atom_6); + DIALA.push_back(DIALA_atom_7); + DIALA.push_back(DIALA_atom_8); + DIALA.push_back(DIALA_atom_9); + DIALA.push_back(DIALA_atom_10); + DIALA.push_back(DIALA_atom_11); + DIALA.push_back(DIALA_atom_12); + DIALA.push_back(DIALA_atom_13); + DIALA.push_back(DIALA_atom_14); + DIALA.push_back(DIALA_atom_15); + DIALA.push_back(DIALA_atom_16); + DIALA.push_back(DIALA_atom_17); + DIALA.push_back(DIALA_atom_18); + DIALA.push_back(DIALA_atom_19); + DIALA.push_back(DIALA_atom_20); + DIALA.push_back(DIALA_atom_21); + DIALA.push_back(DIALA_atom_22); + DIALA.push_back(DIALA_atom_23); + + /* Compare GOMC Parser's PROTA vs our Manual Dialanine */ + + typedef std::vector::const_iterator atomIterator; + std::pair itPair1(ms.kindMap["PROTA"].atoms.cbegin(), DIALA.cbegin()); + for (; itPair1.second != DIALA.cend(); ++itPair1.first, ++itPair1.second){ + EXPECT_EQ(*itPair1.first == *itPair1.second, true); + if (*itPair1.first == *itPair1.second){ + + } else { + std::cout << (*itPair1.first).name << " " << (*itPair1.first).mass << " not equal to " << (*itPair1.second).name << " " << (*itPair1.second).mass << std::endl; + } + } + + std::pair itPair2(ms.kindMap["SPCE"].atoms.cbegin(), SPCE.cbegin()); + for (; itPair2.second != SPCE.cend(); ++itPair2.first, ++itPair2.second){ + EXPECT_EQ(*itPair2.first == *itPair2.second, true); + if (*itPair2.first == *itPair2.second){ + + } else { + std::cout << (*itPair2.first).name << " " << (*itPair2.first).mass << " not equal to " << (*itPair2.second).name << " " << (*itPair2.second).mass << std::endl; + } + } + + EXPECT_EQ(ms.kindMap["PROTA"].isMultiResidue, true); + EXPECT_EQ(ms.kindMap["SPCE"].isMultiResidue, false); + +} +