In case you don't need to impose any restraints you can avoid installing Rosetta by using the YASARA minimization server:
http://www.yasara.com/minimizationserver.htm The YASARA self-parameterized ff ranks very high in the recent CASP experiments, and in my experience it slightly outperforms Rosetta all-atom scoring function. Thomas 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. > cheer > marco > > On 17 May 2011 12:20, Thomas Evangelidis <[email protected]> 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 <[email protected]> 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 [email protected] >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> 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 [email protected]. >>> 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: [email protected] >> >> [email protected] >> >> >> website: https://sites.google.com/site/thomasevangelidishomepage/ >> >> >> >> >
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