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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.<o:p></o:p></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? <o:p></o:p></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'><o:p> </o:p></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'>- Chuan<o:p></o:p></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'><o:p> </o:p></span></font></p>
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<p class=MsoNormal align=left style='text-align:left'><b><font size=2
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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'>
gmx-users-bounces@gromacs.org [mailto:gmx-users-bounces@gromacs.org] </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'> <st1:chsdate
IsROCDate="False" IsLunarDate="False" Day="20" Month="4" Year="2011" w:st="on">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></st1:chsdate>
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'><o:p></o:p></span></font></p>
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<p class=MsoNormal align=left style='text-align:left'><font size=2 color=black
face="Times New Roman"><span lang=EN-US style='font-size:10.5pt'><o:p> </o:p></span></font></p>
<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: <o:p></o:p></span></font></p>
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</xml><![endif]-->Dear gmx-users,<u5:p></u5:p></span></font><span lang=EN-US><o:p></o:p></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!<u5:p></u5:p></span></font><span
lang=EN-US><o:p></o:p></span></p>
<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>
Leap in the AmberTools package is good for this.<br>
<br>
Mark<o:p></o:p></span></font></p>
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