I think you can produce a loop of 42 aminoacids by using PYMOL software,It can produce a loop and it's result is a pdb file. Besides,when you could produce your loop you can use it in your folding process.because it is affected by other parts of protein as you said. I think this can be a good approximation to what you want to do. Best
On Mon, Nov 22, 2010 at 3:57 PM, Thomas Evangelidis <teva...@gmail.com>wrote: > 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 >> > > > -- > 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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