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xtb dock geometry "exploding" during optimization using GFN-FF #1132

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camattelaer opened this issue Nov 23, 2024 · 0 comments
Open

xtb dock geometry "exploding" during optimization using GFN-FF #1132

camattelaer opened this issue Nov 23, 2024 · 0 comments
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unconfirmed This report has not yet been confirmed by the developers

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@camattelaer
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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.

To Reproduce
Steps to reproduce the behaviour:

  1. 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

  2. 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.

@camattelaer camattelaer added the unconfirmed This report has not yet been confirmed by the developers label Nov 23, 2024
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