grimme-lab
xtb dock geometry "exploding" during optimization using GFN-FF
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:
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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
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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.
Hi, Thanks for your report. It appears that only the optimization of the pocket search results is problematic, while the rest works fine. Since the pocket search often does not significantly enhance results, I recommend avoiding it for such cases until the issue is fixed.
