Finding input for compute_vina_maps given a reference ligand

[and-tos]

Is there a (python) tool in Vina to obtain the input for the compute_vina_maps method, i.e. center and boundaries of the docking box, given a reference ligand?

[diogomart]

Yes, in mk_prepare_receptor.py (docs), the resulting box will include all the atoms in the file specified with --box_enveloping with a minimum distance, specified by --padding, between any atom and any face of the docking box. For example:

mk_prepare_receptor.py -i dna.cif -o receptor -j -p --box_enveloping some_atoms.pdb --padding 8

[diogomart]

Passing also -v will trigger writing a file with the box specs in vina's config format.