> > 3. QMMM+NMA (Yao Yao) > > Hi Gmxers, > > I am wondering if NMA has been introduced into QMMM part of gromacs. > I am trying to get vibrational frequencies of proteins by normal mode > analysis (NMA) in the framework of QMMM.
This is not possible, unless your system is so small that you can evaluate the hessian numerically. Gerrit > > Thanks, > > Yao > > va...@gmail.com> > Subject: Re: [gmx-users] about side chain and structure rifinement > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <banlktikhcj_envjhklzffnk5drkedvb...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > 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.miel...@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@gromacs.org >> 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 gmx-users-requ...@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: tev...@bioacademy.gr > > teva...@gmail.com > > > website: https://sites.google.com/site/thomasevangelidishomepage/ > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20110517/d166fd58/attachment.html > > ------------------------------ > > -- > gmx-users mailing list > gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > > End of gmx-users Digest, Vol 85, Issue 114 > ****************************************** -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
