[Chimera-users] command line mode

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 1 10:36:33 PST 2008

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    

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!
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

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

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