[Chimera-users] Loading multiple ligand mol2 files for AV

[Elaine Meng]

Hi Leif,
It sounds like you should get the Autodock Vina software installed on your own system to run multiple-ligand docking directly (not via the Chimera interface).  Here is the Autodock Vina website:
<http://vina.scripps.edu/>

Chimera uses an Autodock Vina web service (provided by a different lab) that allows only docking one ligand at a time with not very much sampling of otrientations/conformations, so as not overwhelm their resources.  Thus, the Chimera interface options only allow for docking one ligand at a time with not very much sampling, and is really not meant to be twisted into running what is effectively ligand database docking.  Also you will not get a very good ranking if you don’t sample each ligand very much.  If you use Autodock Vina directly it is a different setup than a series of single-ligand docking runs. 

Chimera Vina interface:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>

However, you can use Chimera for the ligand prep.  You’d have to figure out the command(s) to prep a single ligand structure: could be something like open, addh, addcharge, minimize (with various command options, see their manual pages).  Command manual pages:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

Then, you can construct a script that runs through multiple such files and runs the command(s) as outlined here:
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Sep 26, 2018, at 8:08 AM, Leif Peterson <leifepeterson at sbcglobal.net> wrote:
> 
> Is it possible to load multiple mol2 files, and add H, equlibrate charges, then energy minimize all if the ligands in batch mode, then save all of them to pdbqt files?  Then, loop through all of the ligands using AV on each to get sorted docking results.  Reason I ask is because almost all resources available on multiple ligand use with AD and AV seem outdated, developers moved on, and am hitting dead ends and pages not found.