Using .sdf file as input for geometry optimization generates no output file #563
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jjkowalewski
added
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unconfirmed
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You didn't tell |
awvwgk
added
support
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Thanks for your help. I went ahead and added the --opt flag to the call and did get xtbblast.sdf, however, the optimization stopped in error.
Output ######################################################################## |
|
Looks like you are using an older version of Output of xtb 6.4.1 |
|
Thanks. When doing the install through conda, it doesn't seem like version
6.4.1 is available (I used conda forge and conda)
and only retrieve 6.3.3. When I explicitly request that version in the
conda command, xtb is not found. Is this a version that I have to compile?
…On Sun, Jan 23, 2022 at 12:14 PM Sebastian Ehlert ***@***.***> wrote:
Looks like you are using an older version of xtb, using the latest
version seems to work fine, maybe it is worth upgrading.
Output of xtb 6.4.1
❯ xtb bug563.sdf --namespace bug563 --opt --gfnff --alpb water
-----------------------------------------------------------
| ===================== |
| x T B |
| ===================== |
| S. Grimme |
| Mulliken Center for Theoretical Chemistry |
| University of Bonn |
-----------------------------------------------------------
* xtb version 6.4.1 (afa7bdf) compiled by ***@***.***' on 2021-06-10
xtb is free software: you can redistribute it and/or modify it under
the terms of the GNU Lesser General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
xtb is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Lesser General Public License for more details.
Cite this work as:
* C. Bannwarth, E. Caldeweyher, S. Ehlert, A. Hansen, P. Pracht,
J. Seibert, S. Spicher, S. Grimme, WIREs Comput. Mol. Sci., 2020, 11,
e01493. DOI: 10.1002/wcms.1493
for GFN2-xTB:
* C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019,
15, 1652-1671. DOI: 10.1021/acs.jctc.8b01176
for GFN1-xTB:
* S. Grimme, C. Bannwarth, P. Shushkov, J. Chem. Theory Comput., 2017,
13, 1989-2009. DOI: 10.1021/acs.jctc.7b00118
for GFN0-xTB:
* P. Pracht, E. Caldeweyher, S. Ehlert, S. Grimme, ChemRxiv, 2019, preprint.
DOI: 10.26434/chemrxiv.8326202.v1
for GFN-FF:
* S. Spicher and S. Grimme, Angew. Chem. Int. Ed., 2020, 59, 15665-15673.
DOI: 10.1002/anie.202004239
for DFT-D4:
* E. Caldeweyher, C. Bannwarth and S. Grimme, J. Chem. Phys., 2017,
147, 034112. DOI: 10.1063/1.4993215
* E. Caldeweyher, S. Ehlert, A. Hansen, H. Neugebauer, S. Spicher,
C. Bannwarth and S. Grimme, J. Chem. Phys., 2019, 150, 154122.
DOI: 10.1063/1.5090222
* E. Caldeweyher, J.-M. Mewes, S. Ehlert and S. Grimme, Phys. Chem. Chem. Phys.
2020, 22, 8499-8512. DOI: 10.1039/D0CP00502A
for sTDA-xTB:
* S. Grimme and C. Bannwarth, J. Chem. Phys., 2016, 145, 054103.
DOI: 10.1063/1.4959605
in the mass-spec context:
* V. Asgeirsson, C. Bauer and S. Grimme, Chem. Sci., 2017, 8, 4879.
DOI: 10.1039/c7sc00601b
* J. Koopman and S. Grimme, ACS Omega 2019, 4, 12, 15120-15133.
DOI: 10.1021/acsomega.9b02011
for metadynamics refer to:
* S. Grimme, J. Chem. Theory Comput., 2019, 155, 2847-2862
DOI: 10.1021/acs.jctc.9b00143
for SPH calculations refer to:
* S. Spicher and S. Grimme, J. Chem. Theory Comput., 2021, 17, 1701-1714
DOI: 10.1021/acs.jctc.0c01306
with help from (in alphabetical order)
P. Atkinson, C. Bannwarth, F. Bohle, G. Brandenburg, E. Caldeweyher
M. Checinski, S. Dohm, S. Ehlert, S. Ehrlich, I. Gerasimov, J. Koopman
C. Lavigne, S. Lehtola, F. März, M. Müller, F. Musil, H. Neugebauer
J. Pisarek, C. Plett, P. Pracht, J. Seibert, P. Shushkov, S. Spicher
M. Stahn, M. Steiner, T. Strunk, J. Stückrath, T. Rose, and J. Unsleber
* started run on 2022/01/23 at 21:12:04.322
-------------------------------------------------
| Calculation Setup |
-------------------------------------------------
program call : xtb bug563.sdf --namespace bug563 --opt --gfnff --alpb water
calculation namespace : bug563
coordinate file : bug563.sdf
omp threads : 4
number of atoms : 20
number of electrons : 58
charge : 0
spin : 0.0
first test random number : 0.24597449084177
ID Z sym. atoms
1 8 O 1, 2
2 7 N 3
3 6 C 4-11
4 1 H 12-20
==================== Thresholds ====================
CN : 150.00000
rep : 500.00000
disp: 2500.00000
HB1 : 250.00000
HB2 : 450.00000
Pauling EN used:
Z : 1 EN : 2.20
Z : 6 EN : 2.55
Z : 7 EN : 3.04
Z : 8 EN : 3.44
electric field strengths (au): 0.000
-------------------------------------------------
| Force Field Initialization |
-------------------------------------------------
distances ...
----------------------------------------
generating topology and atomic info file ...
pair mat ...
computing topology distances matrix with Floyd-Warshall algo ...
making topology EEQ charges ...
#fragments for EEQ constrain: 1
----------------------------------------
generating topology and atomic info file ...
pair mat ...
computing topology distances matrix with Floyd-Warshall algo ...
making topology EEQ charges ...
#fragments for EEQ constrain: 1
rings ...
# BATM 152
# H in HB 9
doing iterative Hueckel for 1 subsystem(s) ...
atom neighbors erfCN metchar sp-hybrid imet pi qest coordinates
1 O 2 1.92 0.00 3 0 1 -0.324 4.005652 1.641983 -0.591295
2 O 1 0.98 0.00 2 0 1 -0.379 3.569125 -2.341748 1.100954
3 N 3 2.79 0.00 3 0 1 -0.285 -0.995508 -4.347692 -0.437094
4 C 3 2.82 0.00 2 0 1 0.010 -0.073321 0.136060 0.154958
5 C 3 2.82 0.00 2 0 1 0.057 -1.809224 -1.816027 -0.198421
6 C 3 2.81 0.00 2 0 1 -0.014 -0.915950 2.623129 0.385315
7 C 3 2.81 0.00 2 0 1 -0.020 -4.387566 -1.280667 -0.321253
8 C 3 2.81 0.00 2 0 1 -0.019 -3.494103 3.158110 0.262294
9 C 3 2.81 0.00 2 0 1 -0.023 -5.230006 1.206212 -0.091085
10 C 3 2.81 0.00 2 0 1 0.220 2.632388 -0.360182 0.291396
11 C 4 3.49 0.00 3 0 0 0.041 6.698323 1.381012 -0.556335
12 H 1 0.97 0.00 0 0 0 0.066 0.382103 4.185365 0.690128
13 H 1 0.97 0.00 0 0 0 0.064 -5.760830 -2.783566 -0.595642
14 H 1 0.97 0.00 0 0 0 0.062 -4.151350 5.093567 0.448243
15 H 1 0.97 0.00 0 0 0 0.060 -7.237272 1.623086 -0.185004
16 H 1 0.98 0.00 0 0 0 0.145 0.861337 -4.789510 -0.378323
17 H 1 0.98 0.00 0 0 0 0.145 -2.284112 -5.736074 -0.694852
18 H 1 0.97 0.00 0 0 0 0.065 7.276012 -0.206358 -1.748374
19 H 1 0.97 0.00 0 0 0 0.065 7.363317 1.117962 1.383468
20 H 1 0.97 0.00 0 0 0 0.065 7.522810 3.117103 -1.313549
#atoms : 20
#bonds : 20
#angl : 31
#tors : 45
#nmol : 1
#optfrag : 1
-------------------------------------------------
| G F N - F F |
| A general generic force-field |
| Version 1.0.3 |
-------------------------------------------------
* Solvation model: ALPB
Solvent water
Parameter file internal GFN-FF/ALPB
Dielectric constant 8.0200E+01
Reference state gsolv [1 M gas/solution]
Free energy shift 3.6494E-04 Eh 2.2900E-01 kcal/mol
Temperature 2.9815E+02 K
Density 1.0000E+00 kg/L
Solvent mass 1.8000E+01 g/mol
Interaction kernel P16
Born radius scaling (c1) 1.5056E+00
Born radii integrator GBOBC
Born offset 0.0000E+00 a0 0.0000E+00 AA
H-bond correction true
Ion screening false
Surface tension 1.0000E-05 Eh 1.5569E+01 dyn/cm
Grid points 230 per atom
nhb123 286 38 0
E+G (total) 0 d, 0 h, 0 min, 0.002 sec
distance/D3 list ... 0 min, 0.000 sec ( 0.252%)
non bonded repulsion ... 0 min, 0.000 sec ( 1.185%)
dCN ... 0 min, 0.000 sec ( 1.673%)
EEQ energy and q ... 0 min, 0.000 sec ( 2.295%)
D3 ... 0 min, 0.000 sec ( 10.055%)
EEQ gradient ... 0 min, 0.000 sec ( 3.850%)
bonds ... 0 min, 0.000 sec ( 18.318%)
bend and torsion ... 0 min, 0.000 sec ( 2.295%)
bonded ATM ... 0 min, 0.000 sec ( 0.489%)
HB/XB (incl list setup) ... 0 min, 0.000 sec ( 7.715%)
GBSA ... 0 min, 0.001 sec ( 50.541%)
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -3.799732885205 Eh ::
:: total w/o Gsolv -3.780905154557 Eh ::
:: total w/o Gsasa/hb -3.792410021347 Eh ::
:: gradient norm 0.075658228897 Eh/a0 ::
::.................................................::
:: bond energy -3.874953693698 Eh ::
:: angle energy 0.010958965312 Eh ::
:: torsion energy 0.001669764245 Eh ::
:: repulsion energy 0.236889714200 Eh ::
:: electrostat energy -0.137919544943 Eh ::
:: dispersion energy -0.012737588064 Eh ::
:: HB energy -0.000088415834 Eh ::
:: XB energy 0.000000000000 Eh ::
:: bonded atm energy -0.004724355775 Eh ::
:: external energy 0.000000000000 Eh ::
:: -> Gsolv -0.018827730648 Eh ::
:: -> Gborn -0.011504866790 Eh ::
:: -> Gsasa 0.000582734947 Eh ::
:: -> Ghb -0.008270538059 Eh ::
:: -> Gshift 0.000364939255 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge 0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
-----------------------------------------------------------
| ===================== |
| A N C O P T |
| ===================== |
| Approximate Normal Coordinate |
| Rational Function Optimizer |
-----------------------------------------------------------
...................................................
: SETUP :
:.................................................:
: optimization level normal :
: max. optcycles 200 :
: ANC micro-cycles 20 :
: degrees of freedom 54 :
:.................................................:
: RF solver davidson :
: write xtbopt.log true :
: linear? false :
: energy convergence 0.5000000E-05 Eh :
: grad. convergence 0.1000000E-02 Eh/α :
: maximium RF displ. 1.0000000 :
: Hlow (freq-cutoff) 0.1000000E-01 :
: Hmax (freq-cutoff) 5.0000000 :
: S6 in model hess. 20.0000000 :
...................................................
generating ANC from model Hessian ...
Using GFN-FF Lindh-Hessian
Shifting diagonal of input Hessian by 5.608644366747746E-003
Lowest eigenvalues of input Hessian
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.010000 0.011162 0.012197 0.022151 0.023357 0.032173
0.037923 0.046071 0.048707 0.054231 0.073583 0.081692
Highest eigenvalues
2.329050 2.343611 2.412493 2.651511 2.874854 2.969914
........................................................................
.............................. CYCLE 1 ..............................
........................................................................
* total energy : -3.7997329 Eh change 0.0000000E+00 Eh
gradient norm : 0.0756582 Eh/α predicted 0.0000000E+00 ( NaN%)
displ. norm : 0.1994910 α lambda -0.5446631E-02
maximum displ.: 0.0940510 α in ANC's #8, #3, #4, ...
........................................................................
.............................. CYCLE 2 ..............................
........................................................................
* total energy : -3.8039619 Eh change -0.4228992E-02 Eh
gradient norm : 0.0413251 Eh/α predicted -0.2837149E-02 ( -32.91%)
displ. norm : 0.3020235 α lambda -0.4108471E-02
maximum displ.: 0.1619028 α in ANC's #3, #4, #8, ...
........................................................................
.............................. CYCLE 3 ..............................
........................................................................
* total energy : -3.8063943 Eh change -0.2432389E-02 Eh
gradient norm : 0.0142726 Eh/α predicted -0.2241705E-02 ( -7.84%)
displ. norm : 0.1873763 α lambda -0.7082854E-03
maximum displ.: 0.1318069 α in ANC's #3, #4, #8, ...
........................................................................
.............................. CYCLE 4 ..............................
........................................................................
* total energy : -3.8069399 Eh change -0.5455893E-03 Eh
gradient norm : 0.0135131 Eh/α predicted -0.3665783E-03 ( -32.81%)
displ. norm : 0.2641535 α lambda -0.7187510E-03
maximum displ.: 0.1964187 α in ANC's #3, #4, #6, ...
........................................................................
.............................. CYCLE 5 ..............................
........................................................................
* total energy : -3.8073713 Eh change -0.4314170E-03 Eh
gradient norm : 0.0094300 Eh/α predicted -0.3844527E-03 ( -10.89%)
displ. norm : 0.0853486 α lambda -0.1389973E-03
maximum displ.: 0.0625151 α in ANC's #3, #1, #4, ...
........................................................................
.............................. CYCLE 6 ..............................
........................................................................
* total energy : -3.8074760 Eh change -0.1046997E-03 Eh
gradient norm : 0.0063141 Eh/α predicted -0.7000646E-04 ( -33.14%)
displ. norm : 0.1161180 α lambda -0.1509596E-03
maximum displ.: 0.0755355 α in ANC's #3, #1, #9, ...
........................................................................
.............................. CYCLE 7 ..............................
........................................................................
* total energy : -3.8075827 Eh change -0.1067579E-03 Eh
gradient norm : 0.0044319 Eh/α predicted -0.7649811E-04 ( -28.34%)
displ. norm : 0.1374432 α lambda -0.1095093E-03
maximum displ.: 0.0911719 α in ANC's #1, #3, #9, ...
........................................................................
.............................. CYCLE 8 ..............................
........................................................................
* total energy : -3.8076679 Eh change -0.8518948E-04 Eh
gradient norm : 0.0053034 Eh/α predicted -0.5578952E-04 ( -34.51%)
displ. norm : 0.1907639 α lambda -0.1280273E-03
maximum displ.: 0.1315479 α in ANC's #1, #3, #2, ...
........................................................................
.............................. CYCLE 9 ..............................
........................................................................
* total energy : -3.8077644 Eh change -0.9644142E-04 Eh
gradient norm : 0.0055966 Eh/α predicted -0.6635055E-04 ( -31.20%)
displ. norm : 0.1919863 α lambda -0.1087399E-03
maximum displ.: 0.1387437 α in ANC's #1, #3, #2, ...
........................................................................
.............................. CYCLE 10 ..............................
........................................................................
* total energy : -3.8078391 Eh change -0.7477399E-04 Eh
gradient norm : 0.0049582 Eh/α predicted -0.5639192E-04 ( -24.58%)
displ. norm : 0.1310960 α lambda -0.7334675E-04
maximum displ.: 0.0988226 α in ANC's #1, #3, #2, ...
........................................................................
.............................. CYCLE 11 ..............................
........................................................................
* total energy : -3.8078922 Eh change -0.5308213E-04 Eh
gradient norm : 0.0035480 Eh/α predicted -0.3730474E-04 ( -29.72%)
displ. norm : 0.1584536 α lambda -0.6693414E-04
maximum displ.: 0.1085049 α in ANC's #1, #3, #2, ...
........................................................................
.............................. CYCLE 12 ..............................
........................................................................
* total energy : -3.8079367 Eh change -0.4448559E-04 Eh
gradient norm : 0.0042210 Eh/α predicted -0.3431870E-04 ( -22.85%)
displ. norm : 0.0814287 α lambda -0.6284621E-04
maximum displ.: 0.0530544 α in ANC's #1, #6, #2, ...
........................................................................
.............................. CYCLE 13 ..............................
........................................................................
* total energy : -3.8079602 Eh change -0.2350974E-04 Eh
gradient norm : 0.0041403 Eh/α predicted -0.3163211E-04 ( 34.55%)
displ. norm : 0.1015657 α lambda -0.3557022E-04
maximum displ.: 0.0635521 α in ANC's #3, #1, #2, ...
........................................................................
.............................. CYCLE 14 ..............................
........................................................................
* total energy : -3.8079809 Eh change -0.2065865E-04 Eh
gradient norm : 0.0030924 Eh/α predicted -0.1796894E-04 ( -13.02%)
displ. norm : 0.0257994 α lambda -0.2105785E-04
maximum displ.: 0.0159714 α in ANC's #4, #3, #1, ...
........................................................................
.............................. CYCLE 15 ..............................
........................................................................
* total energy : -3.8079970 Eh change -0.1610084E-04 Eh
gradient norm : 0.0021674 Eh/α predicted -0.1053774E-04 ( -34.55%)
displ. norm : 0.0963153 α lambda -0.3043871E-04
maximum displ.: 0.0608304 α in ANC's #1, #3, #2, ...
........................................................................
.............................. CYCLE 16 ..............................
........................................................................
* total energy : -3.8080176 Eh change -0.2058597E-04 Eh
gradient norm : 0.0028226 Eh/α predicted -0.1536157E-04 ( -25.38%)
displ. norm : 0.1070903 α lambda -0.2197169E-04
maximum displ.: 0.0759440 α in ANC's #1, #3, #2, ...
........................................................................
.............................. CYCLE 17 ..............................
........................................................................
* total energy : -3.8080337 Eh change -0.1614077E-04 Eh
gradient norm : 0.0027191 Eh/α predicted -0.1111267E-04 ( -31.15%)
displ. norm : 0.1356204 α lambda -0.2284053E-04
maximum displ.: 0.0918389 α in ANC's #1, #3, #2, ...
........................................................................
.............................. CYCLE 18 ..............................
........................................................................
* total energy : -3.8080492 Eh change -0.1549865E-04 Eh
gradient norm : 0.0024793 Eh/α predicted -0.1163364E-04 ( -24.94%)
displ. norm : 0.0699548 α lambda -0.1885794E-04
maximum displ.: 0.0439058 α in ANC's #1, #3, #2, ...
........................................................................
.............................. CYCLE 19 ..............................
........................................................................
* total energy : -3.8080599 Eh change -0.1066369E-04 Eh
gradient norm : 0.0020273 Eh/α predicted -0.9477542E-05 ( -11.12%)
displ. norm : 0.1353107 α lambda -0.1532730E-04
maximum displ.: 0.0840355 α in ANC's #3, #1, #2, ...
........................................................................
.............................. CYCLE 20 ..............................
........................................................................
* total energy : -3.8080662 Eh change -0.6331457E-05 Eh
gradient norm : 0.0025107 Eh/α predicted -0.7809505E-05 ( 23.34%)
displ. norm : 0.0282770 α lambda -0.1256761E-04
maximum displ.: 0.0207758 α in ANC's #1, #4, #2, ...
* RMSD in coord.: 0.4896712 α energy gain -0.8333307E-02 Eh
generating ANC from model Hessian ...
Using GFN-FF Lindh-Hessian
Shifting diagonal of input Hessian by 4.216134266720032E-003
Lowest eigenvalues of input Hessian
0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
0.010000 0.010488 0.013003 0.024195 0.026649 0.033249
0.040055 0.045668 0.054693 0.065245 0.081060 0.086395
Highest eigenvalues
2.429011 2.457605 2.503415 2.744172 2.954389 3.021850
........................................................................
.............................. CYCLE 21 ..............................
........................................................................
* total energy : -3.8080757 Eh change -0.9479579E-05 Eh
gradient norm : 0.0017696 Eh/α predicted 0.0000000E+00 (-100.00%)
displ. norm : 0.0200145 α lambda -0.3213613E-05
maximum displ.: 0.0126051 α in ANC's #4, #5, #3, ...
........................................................................
.............................. CYCLE 22 ..............................
........................................................................
* total energy : -3.8080840 Eh change -0.8313665E-05 Eh
gradient norm : 0.0005956 Eh/α predicted -0.3574639E-05 ( -57.00%)
displ. norm : 0.0471766 α lambda -0.9402436E-05
maximum displ.: 0.0286895 α in ANC's #4, #5, #3, ...
........................................................................
.............................. CYCLE 23 ..............................
........................................................................
* total energy : -3.8080934 Eh change -0.9448300E-05 Eh
gradient norm : 0.0012484 Eh/α predicted -0.4706942E-05 ( -50.18%)
displ. norm : 0.0425288 α lambda -0.4915190E-05
maximum displ.: 0.0264652 α in ANC's #5, #3, #4, ...
........................................................................
.............................. CYCLE 24 ..............................
........................................................................
* total energy : -3.8080991 Eh change -0.5699809E-05 Eh
gradient norm : 0.0013387 Eh/α predicted -0.2483006E-05 ( -56.44%)
displ. norm : 0.0623835 α lambda -0.6091033E-05
maximum displ.: 0.0390599 α in ANC's #3, #5, #4, ...
........................................................................
.............................. CYCLE 25 ..............................
........................................................................
* total energy : -3.8081052 Eh change -0.6103364E-05 Eh
gradient norm : 0.0009218 Eh/α predicted -0.3058038E-05 ( -49.90%)
displ. norm : 0.0393895 α lambda -0.3081652E-05
maximum displ.: 0.0296633 α in ANC's #3, #5, #4, ...
........................................................................
.............................. CYCLE 26 ..............................
........................................................................
* total energy : -3.8081087 Eh change -0.3495004E-05 Eh
gradient norm : 0.0006883 Eh/α predicted -0.1568604E-05 ( -55.12%)
displ. norm : 0.0451553 α lambda -0.3347831E-05
maximum displ.: 0.0379971 α in ANC's #3, #5, #2, ...
*** GEOMETRY OPTIMIZATION CONVERGED AFTER 26 ITERATIONS ***
------------------------------------------------------------------------
total energy gain : -0.0083758 Eh -5.2559 kcal/mol
total RMSD : 0.5015331 a0 0.2654 Å
total power (kW/mol): -0.8457993 (step) -441.2468 (real)
------------------------------------------------------------------------
ANCopt (total) 0 d, 0 h, 0 min, 0.050 sec
optimizer setup ... 0 min, 0.002 sec ( 4.295%)
model hessian ... 0 min, 0.003 sec ( 5.753%)
ANC generation ... 0 min, 0.005 sec ( 10.524%)
coordinate transformation ... 0 min, 0.000 sec ( 0.512%)
single point calculation ... 0 min, 0.020 sec ( 39.912%)
optimization log ... 0 min, 0.002 sec ( 4.617%)
hessian update ... 0 min, 0.000 sec ( 0.795%)
rational function ... 0 min, 0.006 sec ( 11.207%)
================
final structure:
================
8635
xtb 01232221123D
xtb: 6.4.1 (afa7bdf)
20 20 0 0 0 999 V2000
2.1862 1.0343 -0.1092 O 0 0 0 0 0 0 0 0 0 0 0 0
1.9051 -1.2272 -0.0651 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.5362 -2.2719 -0.2018 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.0398 0.1057 -0.0517 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9595 -0.9662 -0.1023 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.5220 1.4042 0.0257 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3283 -0.6756 -0.0620 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8718 1.6640 0.0602 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.7767 0.6185 0.0177 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4255 -0.1083 -0.0770 C 0 0 0 0 0 0 0 0 0 0 0 0
3.5446 0.7170 -0.1316 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1881 2.2130 0.0580 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.0311 -1.4886 -0.1002 H 0 0 0 0 0 0 0 0 0 0 0 0
-2.2249 2.6801 0.1209 H 0 0 0 0 0 0 0 0 0 0 0 0
-3.8344 0.8220 0.0461 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4430 -2.4994 -0.1529 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1446 -3.0660 -0.1286 H 0 0 0 0 0 0 0 0 0 0 0 0
3.7511 0.0862 -0.9995 H 0 0 0 0 0 0 0 0 0 0 0 0
3.8012 0.1773 0.7830 H 0 0 0 0 0 0 0 0 0 0 0 0
4.1264 1.6390 -0.1970 H 0 0 0 0 0 0 0 0 0 0 0 0
1 10 1 0 0 0 0
1 11 1 0 0 0 0
2 10 2 0 0 0 0
3 5 1 0 0 0 0
3 16 1 0 0 0 0
3 17 1 0 0 0 0
4 5 1 0 0 0 0
4 6 2 0 0 0 0
4 10 1 0 0 0 0
5 7 2 0 0 0 0
6 8 1 0 0 0 0
6 12 1 0 0 0 0
7 9 1 0 0 0 0
7 13 1 0 0 0 0
8 9 2 0 0 0 0
8 14 1 0 0 0 0
9 15 1 0 0 0 0
11 18 1 0 0 0 0
11 19 1 0 0 0 0
11 20 1 0 0 0 0
M END
> <PUBCHEM_COMPOUND_CID>
8635
> <PUBCHEM_CONFORMER_RMSD>
0.4
> <PUBCHEM_CONFORMER_DIVERSEORDER>
1
6
4
3
5
2
> <PUBCHEM_MMFF94_PARTIAL_CHARGES>
17
1 -0.43
10 0.63
11 0.28
12 0.15
13 0.15
14 0.15
15 0.15
16 0.4
17 0.4
2 -0.57
3 -0.9
4 0.09
5 0.1
6 -0.15
7 -0.15
8 -0.15
9 -0.15
> <PUBCHEM_EFFECTIVE_ROTOR_COUNT>
2
> <PUBCHEM_PHARMACOPHORE_FEATURES>
4
1 2 acceptor
1 3 cation
1 3 donor
6 4 5 6 7 8 9 rings
> <PUBCHEM_HEAVY_ATOM_COUNT>
11
> <PUBCHEM_ATOM_DEF_STEREO_COUNT>
0
> <PUBCHEM_ATOM_UDEF_STEREO_COUNT>
0
> <PUBCHEM_BOND_DEF_STEREO_COUNT>
0
> <PUBCHEM_BOND_UDEF_STEREO_COUNT>
0
> <PUBCHEM_ISOTOPIC_ATOM_COUNT>
0
> <PUBCHEM_COMPONENT_COUNT>
1
> <PUBCHEM_CACTVS_TAUTO_COUNT>
2
> <PUBCHEM_CONFORMER_ID>
000021BB00000001
> <PUBCHEM_MMFF94_ENERGY>
43.1026
> <PUBCHEM_FEATURE_SELFOVERLAP>
20.297
> <PUBCHEM_SHAPE_FINGERPRINT>
12716758 59 18343305889887347114
12897270 3 18411701023409470948
13024252 1 14345789470212566053
13380535 76 18411980252266102302
14325111 11 18410575041724195808
15775835 57 18336271158336852344
16945 1 18339073908038920641
20645464 45 17631995533900384570
20871998 184 18129668645832792287
21040471 1 18413101740940539787
23402539 116 18271798059910415861
23552423 10 18265050219770354979
23559900 14 18272655680177923668
241688 4 16466147809746459307
2748010 2 18338800005063101197
369184 2 16008742528554128737
5084963 1 18058444292545403963
528886 8 18411414008030372129
6333449 129 18341893038641130952
7364860 26 18270115696047140194
> <PUBCHEM_SHAPE_MULTIPOLES>
209.66
4.32
1.84
0.65
2.75
0.51
-0.01
-1.2
0.37
-0.51
0
0.05
0
-0.31
> <PUBCHEM_SHAPE_SELFOVERLAP>
436.855
> <PUBCHEM_SHAPE_VOLUME>
119.9
> <PUBCHEM_COORDINATE_TYPE>
2
5
10
$$$$
Bond Distances (Angstroems)
---------------------------
O1-C10=1.3731 O1-C11=1.3951 O2-C10=1.2174 N3-C5=1.3761 N3-H16=1.0064 N3-H17=1.0031
C4-C5=1.4133 C4-C6=1.3873 C4-C10=1.4811 C5-N3=1.3761 C5-C4=1.4133 C5-C7=1.3999
C6-C4=1.3873 C6-C8=1.3750 C6-H12=1.0768 C7-C5=1.3999 C7-C9=1.3718 C7-H13=1.0754
C8-C6=1.3750 C8-C9=1.3834 C8-H14=1.0775 C9-C7=1.3718 C9-C8=1.3834 C9-H15=1.0775
C10-O1=1.3731 C10-O2=1.2174 C10-C4=1.4811 C11-O1=1.3951 C11-H18=1.0926 C11-H19=1.0926
C11-H20=1.0921 H12-C6=1.0768 H13-C7=1.0754 H14-C8=1.0775 H15-C9=1.0775 H16-N3=1.0064
H17-N3=1.0031 H18-C11=1.0926 H19-C11=1.0926 H20-C11=1.0921
C H Rav=1.0835 sigma=0.0078 Rmin=1.0754 Rmax=1.0926 7
C C Rav=1.4017 sigma=0.0350 Rmin=1.3718 Rmax=1.4811 7
N H Rav=1.0048 sigma=0.0017 Rmin=1.0031 Rmax=1.0064 2
N C Rav=1.3761 sigma=0.0000 Rmin=1.3761 Rmax=1.3761 1
O C Rav=1.3285 sigma=0.0791 Rmin=1.2174 Rmax=1.3951 3
selected bond angles (degree)
--------------------
C11-O1-C10=110.52 H16-N3-C5=120.68 H17-N3-C5=124.01 H17-N3-H16=114.05
C6-C4-C5=119.06 C10-C4-C5=122.25 C10-C4-C6=118.69 C4-C5-N3=121.47
C7-C5-N3=119.99 C7-C5-C4=118.54 C8-C6-C4=121.29 H12-C6-C4=118.39
H12-C6-C8=120.32 C9-C7-C5=121.14 H13-C7-C5=118.75 H13-C7-C9=120.11
C9-C8-C6=119.91 H14-C8-C6=120.09 H14-C8-C9=120.01 C8-C9-C7=120.06
H15-C9-C7=120.04 H15-C9-C8=119.91 O2-C10-O1=123.15 C4-C10-O1=115.36
C4-C10-O2=121.50
selected dihedral angles (degree)
---------------------------------
C4-C5-N3-H16= 5.85 C4-C5-N3-H17=172.24 C7-C5-N3-H16=185.23 C7-C5-N3-H17=351.62
N3-C5-C4-C6=178.91 N3-C5-C4-C10=358.85 C7-C5-C4-C6=359.52 C7-C5-C4-C10=179.46
C8-C6-C4-C5= 0.31 C8-C6-C4-C10=180.37 H12-C6-C4-C5=180.34 H12-C6-C4-C10= 0.40
C9-C7-C5-N3=180.94 C9-C7-C5-C4= 0.34 H13-C7-C5-N3= 0.61 H13-C7-C5-C4=180.01
C9-C8-C6-C4= 0.00 C9-C8-C6-H12=179.98 H14-C8-C6-C4=179.96 H14-C8-C6-H12=359.93
C8-C9-C7-C5= 0.00 C8-C9-C7-H13=180.32 H15-C9-C7-C5=179.90 H15-C9-C7-H13= 0.24
C7-C9-C8-C6=359.84 C7-C9-C8-H14=179.89 H15-C9-C8-C6=179.92 H15-C9-C8-H14=359.96
O2-C10-O1-C11= 0.27 C4-C10-O1-C11=180.03 O1-C10-C4-C5=175.93 O1-C10-C4-C6=355.87
O2-C10-C4-C5=355.69 O2-C10-C4-C6=175.63
-------------------------------------------------
| Final Singlepoint |
-------------------------------------------------
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: SUMMARY ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
:: total energy -3.808108731975 Eh ::
:: total w/o Gsolv -3.790666413754 Eh ::
:: total w/o Gsasa/hb -3.800413933203 Eh ::
:: gradient norm 0.000688423281 Eh/a0 ::
::.................................................::
:: bond energy -3.892349226845 Eh ::
:: angle energy 0.006090849456 Eh ::
:: torsion energy 0.000267701035 Eh ::
:: repulsion energy 0.256763709294 Eh ::
:: electrostat energy -0.142342063148 Eh ::
:: dispersion energy -0.012768606654 Eh ::
:: HB energy -0.000188715662 Eh ::
:: XB energy 0.000000000000 Eh ::
:: bonded atm energy -0.006140061229 Eh ::
:: external energy 0.000000000000 Eh ::
:: -> Gsolv -0.017442318222 Eh ::
:: -> Gborn -0.009747519450 Eh ::
:: -> Gsasa 0.000327941573 Eh ::
:: -> Ghb -0.008387679600 Eh ::
:: -> Gshift 0.000364939255 Eh ::
:: add. restraining 0.000000000000 Eh ::
:: total charge -0.000000000000 e ::
:::::::::::::::::::::::::::::::::::::::::::::::::::::
-------------------------------------------------
| Property Printout |
-------------------------------------------------
-------------------------------------------------
| Geometry Summary |
-------------------------------------------------
molecular mass/u : 151.1628670
center of mass at/Å : 0.1168656 -0.0079174 -0.0664497
moments of inertia/u·Å² : 0.2335200E+03 0.6050208E+03 0.8348627E+03
rotational constants/cm⁻¹ : 0.7218923E-01 0.2786290E-01 0.2019210E-01
* 19 selected distances
# Z # Z value/Å
3 7 N 5 6 C 1.3761468
4 6 C 5 6 C 1.4133243 (max)
4 6 C 6 6 C 1.3872734
5 6 C 7 6 C 1.3999245
6 6 C 8 6 C 1.3749692
7 6 C 9 6 C 1.3718494
8 6 C 9 6 C 1.3833573
1 8 O 10 6 C 1.3731098
2 8 O 10 6 C 1.2173556
1 8 O 11 6 C 1.3951155
6 6 C 12 1 H 1.0767657
7 6 C 13 1 H 1.0754038
8 6 C 14 1 H 1.0774957
9 6 C 15 1 H 1.0775098
3 7 N 16 1 H 1.0064391
3 7 N 17 1 H 1.0031325 (min)
11 6 C 18 1 H 1.0926176
11 6 C 19 1 H 1.0925554
11 6 C 20 1 H 1.0921491
* 5 distinct bonds (by element types)
Z Z # av. dist./Å max./Å min./Å
1 H 6 C 7 1.0834996 1.0926176 1.0754038
6 C 6 C 6 1.3884497 1.4133243 1.3718494
1 H 7 N 2 1.0047858 1.0064391 1.0031325
6 C 7 N 1 1.3761468 1.3761468 1.3761468
6 C 8 O 3 1.3285270 1.3951155 1.2173556
optimized geometry written to: xtbopt.sdf
-------------------------------------------------
| TOTAL ENERGY -3.808108731975 Eh |
| GRADIENT NORM 0.000688423281 Eh/α |
-------------------------------------------------
########################################################################
[WARNING] Runtime exception occurred
-4- gfnff_ini: Could not initialize fragment charges from file
-3- gfnff_ini: Could not initialize fragment charges from file
-2- gfnff_setup: Could not read topology file.
-1- restart_read_restart_gff: Atom number missmatch in restart file.
########################################################################
------------------------------------------------------------------------
* finished run on 2022/01/23 at 21:12:04.466
------------------------------------------------------------------------
total:
* wall-time: 0 d, 0 h, 0 min, 0.143 sec
* cpu-time: 0 d, 0 h, 0 min, 0.408 sec
* ratio c/w: 2.861 speedup
SCF:
* wall-time: 0 d, 0 h, 0 min, 0.006 sec
* cpu-time: 0 d, 0 h, 0 min, 0.019 sec
* ratio c/w: 3.118 speedup
ANC optimizer:
* wall-time: 0 d, 0 h, 0 min, 0.064 sec
* cpu-time: 0 d, 0 h, 0 min, 0.199 sec
* ratio c/w: 3.119 speedup
normal termination of xtb
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Probably something inside your conda environment might be pinned to an old runtime library. Try creating a fresh one or update the whole environment at once ( |
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Thanks. I updated and the error went away. |
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I am using a .sdf file containing a 3D conformer from PubChem and am performing geometry optimization in water using:
xtb ma.sdf --alpb water --gfnffWhen I run this, I do not get the desired output. The documentation shows .xyz files being used. It is inferred that the program will automatically output in the format of the input in that example. However, I am not getting a .sdf file or any file containing the coordinates as output.
Input file
ma.sdf.txt
output log
out.log
Expected behaviour
Expected to get a .sdf file with updated, optimized coordinates.
Additional context
N/A
The text was updated successfully, but these errors were encountered: