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.<br>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.<br>
I think this can be a good approximation to what you want to do.<br>Best<br><br><div class="gmail_quote">On Mon, Nov 22, 2010 at 3:57 PM, Thomas Evangelidis <span dir="ltr"><<a href="mailto:tevang3@gmail.com">tevang3@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">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><font color="#888888">Thomas</font><div><div></div><div class="h5"><br><br><br><br><div class="gmail_quote">On 22 November 2010 13:48, ms <span dir="ltr"><<a href="mailto:devicerandom@gmail.com" target="_blank">devicerandom@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>On 22/11/10 11:09, mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; 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>
<br>
<br>
M.<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; 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><br>
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