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Hi,<br>
<br>
It seems like you look into modelling the polypeptide, if you have a
good template you can use pymol ot even insight. If you wish to have
an ab-initio model you can use sybyl or alike.<br>
<br>
Good luck with it,<br>
Itamar<br>
<br>
On 20/04/11 2:36 PM, Liao Chuan wrote:
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<p class="MsoNormal"><font face="Arial" size="1"><span
style="font-size: 9pt; font-family: Arial;" lang="EN-US">Dear
gmx-users,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="1"><span
style="font-size: 9pt; font-family: Arial;" lang="EN-US">I
want to conduct simulations of a protein and its
ligand, a heptapeptide HXXXPAS, where X could be tyrosine,
tryptophan, pheny
alanine, alanine. Thus, I will have to conduct a total
number of 4*4*4=64 runs.
I’ve got the pdb file of the protein, but I have no idea
how to prepare
the pdb files of those 64 heptapeptides with sequences
already known. Is there any
software/script which could convert a polypeptide sequence
to a pdb file? Any
comment is appreciated!<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="1"><span
style="font-size: 9pt; font-family: Arial;" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="1"><span
style="font-size: 9pt; font-family: Arial;" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="1"><span
style="font-size: 9pt; font-family: Arial;" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="1"><span
style="font-size: 9pt; font-family: Arial;" lang="EN-US">-
Chuan <o:p></o:p></span></font></p>
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<br>
<pre class="moz-signature" cols="72">--
"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: <a class="moz-txt-link-abbreviated" href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a>
============================================</pre>
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