[Chimera-users] calculating charges for Dock

Elaine Meng meng at cgl.ucsf.edu
Wed Jun 28 14:19:23 PDT 2006

Hi Josh,
I believe a newer version of Chimera will solve this problem.  Get  
snapshot version 1.2255:


Chimera version 1.2255 includes Antechamber and calls it  
automatically from Dock Prep.  In version 1.2199, Dock Prep only  
added charges to standard residues, as the procedure for nonstandard  
residues was still under development.

On Jun 28, 2006, at 1:50 PM, Joshua D Campbell wrote:

> Hello,
> My name is Josh Campbell and I'm trying to prepare a ligand for  
> docking that is
> made up of non-standard residues using Chimera.  The Dock Prep tool  
> of course
> does not assign charges to non-standard atoms.  I looked at your  
> UserGuide and
> it said that there were other places to calculate non-standard  
> residues using
> the Antechamber module, but I could not find any of these tools  
> anywhere in the
> Chimera program.  If you could give me some clarification as to  
> adding charges
> on non-standard residues, I would be very greatful. I am working  
> with "beta
> version 1 build 2199 2006/01/24".  Thanks.
> Sincerely,
> Josh Campbell
> Harvard Medical School
> Laboratory of Structural Cell Biology
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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

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