With respect to protein folding, I want to fold a 42 amino acid loop (part of a protein domain with known structure) which has no homologous counterpart in PDB. Ab initio servers fail to assign a compact tertiary structure to the loop, so I would like to see how MD tools can cope with this problem. I 'm wondering if there is any way to keep the rest of the protein rigid while running the simulation, cause the loop interacts with the protein surface at many points.Is simulated annealing the right approach? I'd appreciate any advice as I think the time scale of the problem I described is accessible to MD.
thanks in advance, Thomas On 22 November 2010 13:48, ms <deviceran...@gmail.com> wrote: > On 22/11/10 11:09, mohsen ramezanpour wrote: > >> Dear All >> >> I am searching for a tutorial for learning how to do protein folding with >> Gromacs. >> Do any one know such tutorials? >> Please let me know them. >> > > I don't think so because managing to fold a protein in a MD simulation is > no easy task. In theory, if you have a lot of patience and a lot of > computational resources, it's no different from a normal MD simulation, but > good luck even getting *close* to a folded state. > > So, it all depends on what you want really to know, and in this case > several techniques may help you (REMD, metadynamics, etc.) but I think you > have to read a lot of literature to make up your mind on such stuff. > > > M. > > Thanks in advance >> Sincerely >> Mohsen >> >> >> > > -- > Massimo Sandal, Ph.D. > http://devicerandom.org > > -- > 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 >
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