[phenixbb] model minimzation?

Francois Berenger berenger at riken.jp
Fri Sep 2 01:50:59 PDT 2011


On 09/02/2011 05:01 PM, Ralf Grosse-Kunstleve wrote:
> phenix.pdbtools --geometry-regularization
>
> goes in this direction, but our "force fields" really are too primitive
> for use without experimental data. Also, we don't support atom
> selections to keep parts of the model fixed. To get access to such atom
> selections, you could use phenix.refine with a combination of options to
> turn off the use of experimental data, but the same caveat applies. --
> Hope others have suggestions for better tools for your purpose.

Maybe some MD packages: CHARMM, Gromacs, etc.
Also, some patience will be required. ;)

> Ralf
>
> On Fri, Sep 2, 2011 at 12:34 AM, r n <ramme29 at yahoo.com
> <mailto:ramme29 at yahoo.com>> wrote:
>
>     Dear all,
>
>     Is it possible to do force field energy minimization for
>     protein/peptide using Phenix?
>
>     I am interested in doing energy minimization for different side
>     chain rotamers.
>
>     Thanks
>     ram
>
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