Diogo

Tried with a system and can't reproduce. Got very similar first poses and very similar scores (-7.090 vs -7.063). Could you share your files and commands/scripts to reproduce?

In my tests `v.energies()[0][0]` and `v.score()[0]` match exactly. This is the value that is printed to "REMARK VINA RESULT" in output PDBQTs both in v1.1.2 and v1.2.*. Not sure why...

>Which score should I use for the score assessment ? Use `v.energies()[0][0]`. No need to call `v.score()` as it is called inside `v.dock()` to populate the energies that are returned...

Yeah we should reject `--autobox` if used in a docking search. That was the original intent as per the help message: ``` --autobox set maps dimensions based on input ligand(s)...

Hi @Klaborator The only way the coordination geometries affect the scoring is by the addition of a TZ pseudo-atoms to (3,1) geometries. The AD4Zn potentials for oxygen and sulfur H-bond...

The error message says that boost is missing. One way to install it is with conda or mamba or micromamba

I see. The error is still there though. We have not gotten python bindings to work on windows, so maybe it's something else. Sorry, cant help much.

To dock multiple ligands simultaneously from Python pass a list of filenames ```python filenames = ['5x72_ligand_p69.pdbqt','5x72_ligand_p59.pdbqt'] v.set_ligand_from_file(filenames) ```

Not sure this is related, but in the hope it helps, it may be worth testing openmmforcefields `0.11.2` and `0.12.0`. We noticed differences in espaloma charges of symmetric atoms and...

I agree with @rwxayheee. As for further suggestions, if you have only standard amino acids, software for protein structure prediction might be useful, e.g. Alphafold, Rosetta, RFdiffusion.