[Chimera-users] Minimize Structure While keeping charges

Elaine Meng meng at cgl.ucsf.edu
Wed May 16 15:57:38 PDT 2012

Hi Mike,
Unfortunately it is not possible to use the charges directly from a mol2 or pqr file for minimization.  Although reading in a mol2 or pqr file with charges will assign the values as atom attributes, subsequently running miminization will still run Add Charge and assign charges, overwriting those values. 

It is possible to specify your own charges for nonstandard residues (only) using an attribute definition file or Chimera "setattr" commands, as explained here:


At least, those were the only ways I was able to figure out.  Maybe others have come up with some devious workarounds?  
Sorry about that,
Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On May 16, 2012, at 2:48 PM, Michael Tomasini wrote:

> Hello,
>     I was wondering if there was a way to read in charges from a .mol2
> file in order to use those charges in the minimize structure utility.
> By default, it seems that minimize structure adds charges which can
> be a rather time-consuming step.  If I already have the charges in a
> .mol2 file, can these charges simply be used for the minimization?
> Thanks,
> Mike

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