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Describe the bug
During the optimization step, the geometry "explodes" when using GFN-FF, i believe because there is no topology generated - or not as far as i can see.
xtb command: xtb dock receptor.xyz ligand.xyz --optlvl gfnff --opt sloppy --alpb water --pocket --atm &> xtb_docking.out
Please provide all input and output file such that we confirm your report.
Expected behaviour
The topology of structure 1 and structure 2 should be preserved.
Additional context
This does not happen when selecting, e.g., --optlvl gfn1 so is specific to applying the gfn-ff method. This, however, runs a lot slower.
The text was updated successfully, but these errors were encountered:
Describe the bug
During the optimization step, the geometry "explodes" when using GFN-FF, i believe because there is no topology generated - or not as far as i can see.
To Reproduce
Steps to reproduce the behaviour:
structure 1 = receptor_xyz.txt ligand_xyz.txt
structure 2 = ligand_xyz.txt receptor_xyz.txt
part of optimization of first pose using the pocket search = pocket_opt_example_xyz.txt pocket_opt_example_xyz.txt
xtb command:
xtb dock receptor.xyz ligand.xyz --optlvl gfnff --opt sloppy --alpb water --pocket --atm &> xtb_docking.out
Please provide all input and output file such that we confirm your report.
Expected behaviour
The topology of structure 1 and structure 2 should be preserved.
Additional context
This does not happen when selecting, e.g.,
--optlvl gfn1
so is specific to applying the gfn-ff method. This, however, runs a lot slower.The text was updated successfully, but these errors were encountered: