ADL: Ligand/Receptor Preparation for VINA

Oleg Trott trott at scripps.edu
Thu Feb 27 14:10:02 PST 2014


Hi

MGLTools/ADT is not really my department. I hope someone else will
answer your questions. The only thing about input preparation specific
to Vina is that it ignores the partial charges, but you can of course
ignore this safely.

The known ADT bugs are presumably listed in
http://mgldev.scripps.edu/bugs/describecomponents.cgi

MGL Applications/ADT shows 41 results, and Pure Python/AutoDockTools shows 3.

HTH
Oleg

On Wed, Feb 26, 2014 at 3:39 PM, Aaron Schweiger
<aaron.schweiger at gmail.com> wrote:
> 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
> prepare_receptor4.py -- I don't believe this is an issue.  Thoughts?
>
> 2.  I read about an old bug regarding protonation and charge here:
>
> http://mgl.scripps.edu/forum/viewtopic.php?f=9&t=1688
>
> Is this issue still outstanding?
>
> Thanks,
>
>
> Aaron
>
>
> ---------- Forwarded message ----------
> From: "Aaron Schweiger" <aaron.schweiger at gmail.com>
> Date: Feb 23, 2014 3:39 PM
> Subject: ADL: Ligand/Receptor Preparation for VINA
> To: <autodock at scripps.edu>
> Cc:
>
> 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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-- 
Oleg Trott, Ph.D. (Columbia University)

Staff Scientist in the Olson Lab
The Scripps Research Institute

http://olegtrott.com


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