[gmx-users] about side chain and structure rifinement
tevang3 at gmail.com
Tue May 17 12:19:15 CEST 2011
In case you don't need to impose any restraints you can avoid installing
Rosetta by using the YASARA minimization server:
The YASARA self-parameterized ff ranks very high in the recent CASP
experiments, and in my experience it slightly outperforms Rosetta all-atom
Thank you very much to answer me quickly.
> I have already utilized SCRWRL4,
> It have improve some side chain but other not.
> So I thought to improve trough to MD OPLS the rest of structure and
> side chain, too.
> I now try in this way and then I'll send you the results if you're
> interested on it.
> On 17 May 2011 12:20, Thomas Evangelidis <tevang3 at gmail.com> wrote:
>> 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
>>> gmx-users mailing list gmx-users at gromacs.org
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> 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/
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users