[Chimera-users] minimization error
neelagiri.d at gmail.com
Tue Dec 20 14:52:14 PST 2011
Thank you very much!!
On Tue, Dec 20, 2011 at 5:27 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Chimera-users