ADL: Ligand/Receptor Preparation for VINA

Aaron Schweiger aaron.schweiger at gmail.com
Sun Feb 23 12:38:22 PST 2014


Hi,

I had some questions on the preparation of ligands and receptors for ZINC.

#1:  I have retrieved my ligands from zinc.docking.org 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 zinc.docking.org for use
with VINA using prepare_ligand4.py?  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 *prepare_receptor4.py -A checkhydrogens* ....

Otherwise if edits were required, use *prepare_receptor4.py -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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