<div><br></div>Hi Chuan,<div><br></div><div>Leap is a part of Ambertools which is free. See <a href="http://ambermd.org/#AmberTools">http://ambermd.org/#AmberTools</a></div><meta http-equiv="content-type" content="text/html; charset=utf-8"><div>
<br></div><div>Good luck.</div><div><br></div><div>Terry<br><br><div class="gmail_quote">2011/4/20 Liao Chuan <span dir="ltr"><<a href="mailto:liaochuan@tju.edu.cn">liaochuan@tju.edu.cn</a>></span><br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
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<p class="MsoNormal"><font size="1" color="navy" face="Arial"><span lang="EN-US" style="font-size:9.0pt;font-family:Arial;color:navy">HI, Itamer and Mark,
thanks for your prompt replies.</span></font></p>
<p class="MsoNormal"><font size="1" color="navy" face="Arial"><span lang="EN-US" style="font-size:9.0pt;font-family:Arial;color:navy">Pymol, Amber and Sybyl are
commercial software. Any free software/scripts? </span></font></p>
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<p class="MsoNormal"><font size="1" color="navy" face="Arial"><span lang="EN-US" style="font-size:9.0pt;font-family:Arial;color:navy">- Chuan</span></font></p>
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<p class="MsoNormal" align="left" style="text-align:left"><b><font size="2" color="black" face="宋体"><span style="font-size:10.0pt;font-family:SimSun;color:windowtext;font-weight:bold">发件人<span lang="EN-US">:</span></span></font></b><font size="2" color="black" face="宋体"><span lang="EN-US" style="font-size:10.0pt;font-family:SimSun;color:windowtext">
<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a> [mailto:<a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>] </span></font><b><font size="2" color="black" face="宋体"><span style="font-size:10.0pt;font-family:SimSun;color:windowtext;font-weight:bold">代表 </span></font></b><font size="2" color="black" face="宋体"><span lang="EN-US" style="font-size:10.0pt;font-family:SimSun;color:windowtext">Mark Abraham<br>
</span></font><b><font size="2" color="black" face="宋体"><span style="font-size:10.0pt;font-family:SimSun;color:windowtext;font-weight:bold">发送时间<span lang="EN-US">:</span></span></font></b><font size="2" color="black" face="宋体"><span lang="EN-US" style="font-size:10.0pt;font-family:SimSun;color:windowtext"> 2011<span lang="EN-US"><span lang="EN-US">年4</span></span><span lang="EN-US"><span lang="EN-US">月20</span></span><span lang="EN-US"><span lang="EN-US">日</span></span>
13:31<br>
</span></font><b><font size="2" color="black" face="宋体"><span style="font-size:10.0pt;font-family:SimSun;color:windowtext;font-weight:bold">收件人<span lang="EN-US">:</span></span></font></b><font size="2" color="black" face="宋体"><span lang="EN-US" style="font-size:10.0pt;font-family:SimSun;color:windowtext">
Discussion list for GROMACS users<br>
</span></font><b><font size="2" color="black" face="宋体"><span style="font-size:10.0pt;font-family:SimSun;color:windowtext;font-weight:bold">主题<span lang="EN-US">:</span></span></font></b><font size="2" color="black" face="宋体"><span lang="EN-US" style="font-size:10.0pt;font-family:SimSun;color:windowtext"> Re:
[gmx-users] any software which could convert a polypeptidesequence to a pdb
file?</span></font><font size="3" color="black"><span lang="EN-US" style="font-size:12.0pt;color:windowtext"></span></font></p>
</div><div class="im">
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<p class="MsoNormal"><font size="2" color="black" face="Times New Roman"><span lang="EN-US" style="font-size:10.5pt">On 4/20/2011 2:36 PM, Liao Chuan wrote: </span></font></p>
</div><div class="im"><p class="MsoNormal"><font size="1" color="black" face="Arial"><span lang="EN-US" style="font-size:9.0pt;font-family:Arial">Dear gmx-users,</span></font><span lang="EN-US"></span></p>
<p class="MsoNormal"><font size="1" color="black" face="Arial"><span lang="EN-US" style="font-size:9.0pt;font-family:Arial">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!</span></font><span lang="EN-US"></span></p>
</div><p class="MsoNormal" align="left" style="text-align:left"><font size="3" color="black" face="Times New Roman"><span lang="EN-US" style="font-size:12.0pt"><br></span></font></p><div class="im"><font size="3" color="black" face="Times New Roman">
Leap in the AmberTools package is good for this.<br>
<br>
Mark</font></div><p></p>
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