ADL: Ligand/Receptor Preparation for VINA

Aaron Schweiger aaron.schweiger at
Wed Feb 26 15:39:10 PST 2014

I wanted to follow up, in the event there are other novices finding
themselves in the same boat. It appears to me that -A hydrogens does so
independently of charge (again, not surprising given that pH isn't
supplied.)  So that means that adding hydrogens to the receptor isn't
strictly necessary after adjusting charges.  (Dear list, please correct me
if I am wrong.)  However, given that vina was trained using -- I don't believe this is an issue.  Thoughts?

2.  I read about an old bug regarding protonation and charge here:

Is this issue still outstanding?



---------- Forwarded message ----------
From: "Aaron Schweiger" <aaron.schweiger at>
Date: Feb 23, 2014 3:39 PM
Subject: ADL: Ligand/Receptor Preparation for VINA
To: <autodock at>


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

#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?


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