Ligand Preparation / Result Issue with Docking V2

[denizkavi]

When running Uni-Mol Docking V2 via the demo.sh script on a custom protein-ligand, every part of the process seems to complete successfully, but the result file for the ligand is different than the input ligand. Do I need to prep the ligand in a certain way to resolve this?

[joonseonyoon]

I also have a similar issue, but not like that much of above image. Bond lengths are shortened with unfavorable angles. Can I find the docking v1 checkpoint file? Thanks for helps.

[ZhouGengmo]

You can try turning on the --steric-clash-fix parameter in demo.py.
And is it convenient for you to share this sdf file? we would like to test it locally.

[ZhouGengmo]

I also have a similar issue, but not like that much of above image. Bond lengths are shortened with unfavorable angles. Can I find the docking v1 checkpoint file? Thanks for helps.

docking v1 checkpoint is here.
The name is ‘Protein-ligand binding pose prediction’.