ADL: Ligand/Receptor Preparation for VINA

Aaron Schweiger aaron.schweiger at
Mon Feb 24 21:20:44 PST 2014

I was hoping that someone could share how protonation is handled by -- somehow I thought -A hydrogens was performing this
calculation.. But I don't see a pH input: should I be using a different
piece of software to get the right protonation?

On Sun, Feb 23, 2014 at 3:38 PM, Aaron Schweiger
<aaron.schweiger at>wrote:

> Hi,
> I had some questions on the preparation of ligands and receptors for ZINC.
> #1:  I have retrieved my ligands from as .mol2 files.
>  All
> of the files I have looked at contain hydrogens, and some of them have a
> net charge. How do I best prepare a ligand from for use
> with VINA using  Should I exclude those ligands with a
> charge?
> #2:  I am working with multiple receptors retrieved from PDB that each
> require different "fixes" before docking with VINA.  Some are fine as-is
> (they already contain hydrogen).  Some have no hydrogens at all in the .pdb
> file.  Others require removal of ligands or a change of charge (Heme) prior
> to docking.
> I have come up with the following heuristic to decide how to fix-up my
> macro molecule:
> If the receptor requires no removal of ligand or change of charges, prepare
> using * -A checkhydrogens* ....
> Otherwise if edits were required, use * -A hydrogens -p
> ... *as a final step after setting charges and removing ligands, regardless
> of whether the original file contained hydrogens.   (???)
> Does that sound about right?
> Thanks,
> Aaron
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