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. <br>
<br>thanks in advance,<br>Thomas<br><br><br><br><div class="gmail_quote">On 22 November 2010 13:48, ms <span dir="ltr"><<a href="mailto:devicerandom@gmail.com">devicerandom@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">On 22/11/10 11:09, mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear All<br>
<br>
I am searching for a tutorial for learning how to do protein folding with<br>
Gromacs.<br>
Do any one know such tutorials?<br>
Please let me know them.<br>
</blockquote>
<br></div>
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.<br>
<br>
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.<div class="im">
<br>
<br>
M.<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Thanks in advance<br>
Sincerely<br>
Mohsen<br>
<br>
<br>
</blockquote>
<br>
<br></div><font color="#888888">
-- <br>
Massimo Sandal, Ph.D.<br>
<a href="http://devicerandom.org" target="_blank">http://devicerandom.org</a></font><div><div></div><div class="h5"><br>
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