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crest-lab / crest

CREST - A program for the automated exploration of low-energy molecular chemical space.
https://crest-lab.github.io/crest-docs/
GNU Lesser General Public License v3.0
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Initial geometry optimization failed #313

Open Jevon-Du opened 5 months ago

Jevon-Du commented 5 months ago

Hello,

I am trying to generate conformations for a cyclic peptide using crest v3.0.1, precompiled binary, commit (1782d7d), xtb version 6.6.1. I get an error when using this command crest xtbtopo.mol --gfn2 -g h2o -T 14, but the program runs fine when using command crest xtbtopo.mol --gfn2 -g chcl3 -T 14. I don't know why. And I tried to use the crest version 2.12(Compatible with xTB version 6.4.0) and it worked fine.

The last two lines of stdout of command crest xtbtopo.mol --gfn2 -g h2o -T 14 is

  Initial geometry optimization failed!
  Please check your input.

test.pdb is the original cyclic peptide structure. xtbopt.pdb and xtbtopo.mol are the cyclic peptide structures after geometry optimization using xtb 6.6.1. The geometry optimization commond is xtb test.pdb --opt. xtbtopo.mol was used as input file of crest v3.0.1. A xyz format of xtbtopo.mol was also used as input file, but I still got the same error as above.

PS: Please change the file suffix txt to the correct format, test.txt to test.pdb, xtbopt.txt to xtbopt.pdb, xtbtopo.txt to xtbtopo.mol.

pprcht commented 5 months ago

Hi, since you get different performance for two different implicit solvents it quite possible is because the implicit solvation implementation in tblite is currently inconsistent with xtb, as mentioned e.g. here #312 There is currently not too much I can do from this side, but I spoke to the tblite developers about it. You could try using --alpb water. This may work, but be aware that the inconsistency is also present in this case.

Jevon-Du commented 4 months ago

Hi,

Thank you for your reply. I tried using --alpb water(crest v3.0.1), but it doesn't work.
OK, I will use crest v2.12 to complete my work.

Thanks again.

satyabratamaiti commented 2 months ago

Initially I optimised the structure with xtb using xtb psu_u_stack.xyz --opt extreme --gfn 2 --alpb water --chrg -1 --uhf 1 then I took the optimised xtbopt.xyz to run crest using: crest --gfn2 --alpb water --chrg -1 --uhf 1 -T 4 but I am getting the error:Command line input: $ crest --gfn2 --alpb water --chrg -1 --uhf 1 -T 4

--gfn2 : Use of GFN2-xTB requested. --alpb water : implicit solvation --chrg -1 --uhf 1 -T 4 (CPUs/Threads selected)

Setting up backup calculator ... done.

Calculation info

User-defined calculation level: : xTB calculation via tblite lib : GFN2-xTB level : Molecular charge : -1 : UHF parameter : 1 : Solvation model : alpb : Solvent : water : Fermi temperature : 300.00000 : Accuracy : 1.00000 : max SCC cycles : 500

Initial Geometry Optimization

Initial geometry optimization failed! Please check your input and, if present, crestopt.log. ERROR STOP

Error termination. Backtrace:

0 0xcecf70 in ???

1 0xced219 in ???

2 0xcee327 in ???

3 0x97a09c in trialoptwarning

at /home/runner/work/crest/crest/src/algos/setuptest.f90:349

4 0x9a6fcd in trialoptcalculator

at /home/runner/work/crest/crest/src/algos/setuptest.f90:312

5 0x7d263c in trialopt_

at /home/runner/work/crest/crest/src/legacy_wrappers.f90:341

6 0x40e116 in crest

at /home/runner/work/crest/crest/src/crest_main.f90:227

7 0x408f7e in main

at /home/runner/work/crest/crest/src/crest_main.f90:26

I am also attaching xipped file containing files.zip input xyz and optimized xyz file. Please give any solution.