[Chimera-users] command line mode

[Elaine Meng]

Hi Snoze,
One of the main  uses of the ZINC database is to generate ligand sets  
for DOCK; I believe you can download mol2 format directly from ZINC,  
and that the molecules already have hydrogens and charges.  See    
http://zinc.docking.org/

But maybe you wanted to use Antechamber inside of Chimera to get  
different charges.  If so, somebody else will have to answer the  
scripting part of your question!
Best
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html


On Feb 1, 2008, at 9:47 AM, snoze pa wrote:

> Dear Chimera Users,
>  How can I use chimera in --nogui mode to screen 1000 compunds from  
> ZINC database and save them in to mol2 format.
> Is there any script so that I can convert preselected 1000 compound  
> from ZINC database and convert them  t o mol2 format so that I can  
> use them in DOCK program.
> thanks in advance