[Dock-fans] Adding charges to a mol2 library

[Scott Brozell]

Hi,

On Mon, 23 Mar 2009, John J. Irwin wrote:

> I recommend molcharge, part of Quakpac, from OpenEye?
>
> Carlos P Sosa wrote:
>>
>> Is there a way to add charges to a library of mol2 ligands?  I can do it
>> via Chimera by processing ligand by ligand but I am wondering if there is
>> a quicker way to deal with a library with about 100 ligands.  Perhaps
>> there are some scripts or utilities available.  Thanks

Presumably, you are pointing and clicking in Chimera instead of
scripting in Chimera.  I do not have such a script handy, but 
probably we could track one down.

Alternatively, Amber score's prepare_amber.pl which uses
amberize_ligand under the hood which calls antechamber
can process ligand libraries.  The simplest approach would
be to invoke it with one of your receptors as well as the ligands:

prepare_amber.pl ligand_mol2_file Receptor_PDB_file

See
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#AMBERScoreInputs

Scott