[gmx-users] protein folding

Thomas Evangelidis tevang3 at gmail.com
Mon Nov 22 13:27:54 CET 2010

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,

On 22 November 2010 13:48, ms <devicerandom at 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 at 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-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20101122/5662c605/attachment.html>

More information about the gromacs.org_gmx-users mailing list