[Chimera-users] Peptide Optimization

[Elaine Meng]

Hi Gus,
Well, there is a "Minimize Structure" tool (menu under Tools... Structure Editing) and corresponding "minimize" command.  For more information, see:
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/minimize.html>

However, if you are asking about the exact settings to use, it depends on your own scientific judgement, the quality of the input structure, and what you plan to do with the output structure.

Also, the minimization is only a local minimization, so the result will depend strongly on the input structure.  Chimera does not do Monte Carlo sampling or molecular dynamics calculations.
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 Jun 21, 2012, at 3:40 PM, Gustavo Souza wrote:

> Hello! has anybody has a clue for a method to optimize a peptide structure (12 aa) using Chimera?
> thanks for help!
> Gus.
>