[Chimera-users] minimization error

[divya neelagiri]

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:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>
>
> ... or could be shown by entering the command:
> help minimize
>
> I hope this helps,
> Elaine
> ----------
> 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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