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/
-- 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
