[gmx-users] about side chain and structure rifinement

Thomas Evangelidis tevang3 at gmail.com
Tue May 17 11:20:19 CEST 2011

A MM ff like OPLS will probably do your job. However CASP experiments show
that knowledge-based potentials like the one Rosetta implements, produce
more physically realistic results. If you only want to improve the
side-chain conformations, I'd suggest to use a program that employs rotamer
libraries like SCWRL4.

On 17 May 2011 12:05, marco miele <marco.miele75 at gmail.com> wrote:

> Hi everyone
> My question is that I have a receptor protein modeled which have some
> problem with side chain angles, I would like to know if is good to
> apply OPLS ff in vacuum to improve the side chain in particularly and
> structure in general.
> what you suggest me.
> Cheer marco
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Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: tevang at bioacademy.gr

          tevang3 at gmail.com

website: https://sites.google.com/site/thomasevangelidishomepage/
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