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On 4/20/2011 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>
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<br>
Leap in the AmberTools package is good for this.<br>
<br>
Mark<br>
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