[Chimera-users] minimization error

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 20 14:27:12 PST 2011

Hi Divya,
Actually freezing does not help, since that atom would still be included in energy calculations and exert forces on other atoms.   I'm guessing it is an ion and not part of a molecule, because I believe GAFF/Antechamber can handle Br that is part of a small organic molecule.  Your choices are to remove the Br ion from your structure, or to change it to Cl (chloride) either by text-editing the input file or doing it in Chimera, for example with commands:

sel Br
setattr a element 17 sel

Although it won't solve this particular problem, for your future reference, the instructions for the "minimize" command including how to freeze are here:

... or could be shown by entering the command:
help minimize

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Dec 20, 2011, at 1:37 PM, divya neelagiri wrote:

> Hello,
> When I tried to minimize a molecule I got this error.
> Atom type Br is not supported ny MMTK. In the previous posts I read that we have to freeze that atom. Can you please tell me how do we do that from the command line.
> Thank you,
> Divya

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