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atomsind.m
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%
% Version 1.0
% Last modified R O Zhurakivsky 2009-01-09
% Created R O Zhurakivsky 2005-09-?
format compact
global GLsdesc GLsdescr GLaspec CG CC CD CH VDV magictorsion
GLsdesc=['a','b','c','d','e','f','g','h','i'];
GLsdescr=['A','B','C','D','E','F','G','H','I','J'];
GLaspec.type= [{'H'};{'C'};{'N'};{'O'};{'F'};{'P'};{'Na'};{'Br'};{'S'};{'Cl'}];
GLaspec.weight= [1;6;7;8;9;15;11;35;16;17];
GLaspec.atommass=[1.00783; 12; 14.00307; 15.99491; 18.99840; 30.97376; 22.98977; 79.904; 32.066; 35.4527]; %amu (from Gaussian)
%Br atom mass 79.904 need to be checked!!!
%091119 values from Êîâàëåíòíûé ðàäèóñ: http://ru.wikipedia.org/wiki/Êàòåãîðèÿ:Õèìè÷åñêèå_ýëåìåíòû
GLaspec.corad = [0.40; 0.77; 0.75; 0.73; 0.72; 1.06; 1.54; 1.14; 1.02; 0.99; ];
%values of covalent radia from "Òàáëèöà Ìåíäåëååâà 2.0" [http://www.kornsoft.narod.ru/progi/mendel.htm]
%value for Na is reduced from 1.54 to 1 for preventing bonds creation
%071018 value for H changed from 0.32 to 0.40
%bond lengths values from Seanger
%CC 1.537
%CN 1.475
%CO 1.426
%CF 1.379
%CP 1.841
%PO 1.71
%critical values for AH...B bonds
%CG.lcritABdist=3.8;
CG.lcritABdist=3.96; %090604 âèá³ðêà ïî 2583 êîíôîðìåðàì 26 ìîëåêóë
%CG.lcritHBdist=2.72; %060608 Van_der_Vaals radii (Bondi,1964 - Seanger)
CG.lcritHBdist=3.18; %090604 âèá³ðêà ïî 2583 êîíôîðìåðàì 26 ìîëåêóë
%CG.lcritAHBang=90;
CG.lcritAHBang=98.5; %090604 âèá³ðêà ïî 2583 êîíôîðìåðàì 26 ìîëåêóë
CC.encoef = 627.5095; %a.e. to kcal/mol energy conversion coefficient (from Gaussian)
CC.ZPEcoefHF631Gd=0.8929; %coefficient to convert ZPE energy
CC.ZPEcoefB3LYP631Gd=0.9804; %coefficient to convert ZPE energy [Foresman Exploring chemistry with electronic struture methods]
CC.freqcoefB3LYP631Gd=0.9613; %coefficient to convert mode's frequinces
CC.ZPEcoefB3LYP631Gdp=0.9804; %coefficient to convert ZPE energy
CC.freqcoefB3LYP631Gdp=0.9608; %coefficient to convert mode's frequinces [http://cccbdb.nist.gov/vsf.asp 2010-0407]
CC.freqcoefMP2FC631Gdp=0.9365;
CD.templatesdir=['..' filesep 'templ'];
CD.bindir='.';
CD.dbdir=['..' filesep 'db'];
CD.xlsdir=['..' filesep 'xls'];
CD.datadir=['..' filesep '..' filesep 'CAN2' filesep 'data'];
CD.xyzdir=['..' filesep 'xyz'];
CD.geomdir=['..' filesep 'geom'];
CD.AIM=['..' filesep 'AIMres'];
CC.h=6.6254E-34; %Plank constant [J*s]
CC.k=1.380658E-23; %Boltzman contsant [J/K]
CC.e=1.602E-19; %charge of electron [C]
CC.amu=1.66035E-27; %amu [kg]
CC.me=5.4876E-4*CC.amu; %mass of electron [kg]
CC.R=8.31436; %Gas contant [J/K/mol]
CC.NA=6.0247E23; %Avogadro constant [1/mol]
CC.c=2.997928E8; %speed of light [m/sec]
CC.l=5.29173E-11; %radius of the first Bohr's orbit [m]
CC.rydberg = 3.288E15; %rydberg constant [sec^-1] [hartree=2*CC.rydrerg*CC.h]
CC.hartree=4.3597482E-18; %[Joules]
CC.freqcoef=CC.c*100; %cm/s - speed of light
%(kT = 208.53cm-1 = 0.0259eV = 0.5962kcal/mol = 9.5004E-4 Hartree , T=300K)
%chemical constants
CH.typOHNdist=1.7; %typical OH...N distance between NH3 molecule and nucleoside
%Wan-der-vaals radii (13. ž.‚. ‡¥ä¨à®¢, .Œ. ‡®àª¨© ‚ -¤¥à-‚ «ìᮢë à ¤¨ãáë ¨ ¨å ¯à¨¬¥¥¨¥ ¢ 娬¨¨ // “á¯¥å¨ å¨¬¨¨. - 1989. - LVIII, ¢ë¯.5. - ‘.713-746.):
%C = 1.71A
%H = 1.16A
%O = 1.29A
%N = 1.50A
%Cl = 1.90A
%S = 1.84A
%Wan-der-vaals radii
%A. Bondi, J. Phys. Chem., 1964, 68, 441. ??
%http://www.webelements.com/webelements/scholar/elements/
%C = 1.70A
%H = 1.20A
%O = 1.52A
%N = 1.55A
%Cl = 1.75A
%S = 1.80A
%A. Bondi, J. Phys. Chem., 1964, 68, 441. ??
%HO=2.72; HN=2.75; HC=2.90; HH=2.40;
VDV.Bondi.C=1.70;
VDV.Bondi.H=1.20;
VDV.Bondi.O=1.52;
VDV.Bondi.N=1.55;
VDV.Bondi.Cl=1.75;
VDV.Bondi.S=1.80;
VDV.Zorkiy.C=1.71;
VDV.Zorkiy.H=1.16;
VDV.Zorkiy.O=1.29;
VDV.Zorkiy.N=1.50;
VDV.Zorkiy.Cl=1.90;
VDV.Zorkiy.S=1.84;
%'new' attribute in molecule data structure legend:
%Y new conformation
%N similar to one exists
%B bad: beta-ribose conformation or something else
%P similar to one in the previous conformation family
%X similar to one in the next conformation family
%T transition state
%F with constrained values
magictorsion(1,:)=[ 6 1 20 21]; %tchi sorted by pind for purines
magictorsion(2,:)=[ 6 1 23 41]; %tchi sorted by pind for pirimidined
magictorsion(3,:)=[19 9 5 4]; %tbeta sorted by pind
magictorsion(4,:)=[ 5 4 3 8]; %tgamma sorted by pind
magictorsion(5,:)=[ 3 4 8 15]; %tepsilon sorted by pind
%Conformation codes
%Y new conformation
%N similar to one exists
%B bad: beta-ribose conformation or something else
%P similar to one in the previous conformation family
%X similar to one in the next conformation family
%T transition state
%D constrained