<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=GB2312" http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 4/20/2011 3:49 PM, Liao Chuan wrote:
<blockquote cite="mid:637EA48363824695A34D60696C712DB7@ERIC"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=GB2312">
<meta name="Generator" content="Microsoft Word 11 (filtered
medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
shape {behavior:url(#default#VML);}
</style>
<![endif]--><o:smarttagtype
namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="chsdate">
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
@font-face
{font-family:SimSun;
panose-1:2 1 6 0 3 1 1 1 1 1;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
text-align:justify;
text-justify:inter-ideograph;
font-size:10.5pt;
font-family:"Times New Roman";
color:black;}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal;
font-family:Arial;
color:windowtext;}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@page Section1
{size:595.3pt 841.9pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;
layout-grid:15.6pt;}
div.Section1
{page:Section1;}
-->
</style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="Section1" style="">
<p class="MsoNormal"><font color="navy" face="Arial" size="1"><span
style="font-size: 9pt; font-family: Arial; color: navy;"
lang="EN-US">HI, Itamer and Mark,
thanks for your prompt replies.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="1"><span
style="font-size: 9pt; font-family: Arial; color: navy;"
lang="EN-US">Pymol, Amber and Sybyl are
commercial software. Any free software/scripts? </span></font></p>
</div>
</o:smarttagtype></blockquote>
<br>
There's a reason I said AmberTools. Google is your friend.<br>
<br>
Mark<br>
<br>
<blockquote cite="mid:637EA48363824695A34D60696C712DB7@ERIC"
type="cite"><o:smarttagtype
namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="chsdate">
<div class="Section1" style="">
<p class="MsoNormal"><font color="navy" face="Arial" size="1"><span
style="font-size: 9pt; font-family: Arial; color: navy;"
lang="EN-US"><o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="1"><span
style="font-size: 9pt; font-family: Arial; color: navy;"
lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="1"><span
style="font-size: 9pt; font-family: Arial; color: navy;"
lang="EN-US">- Chuan<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="1"><span
style="font-size: 9pt; font-family: Arial; color: navy;"
lang="EN-US"><o:p> </o:p></span></font></p>
<div>
<div class="MsoNormal" style="text-align: center;"
align="center"><font color="black" face="Times New Roman"
size="3"><span style="font-size: 12pt; color:
windowtext;" lang="EN-US">
<hr tabindex="-1" width="100%" align="center" size="2">
</span></font></div>
<p class="MsoNormal" style="text-align: left;" align="left"><b><font
color="black" face="宋体" size="2"><span
style="font-size: 10pt; font-family: SimSun; color:
windowtext; font-weight: bold;">发件人<span
lang="EN-US">:</span></span></font></b><font
color="black" face="宋体" size="2"><span style="font-size:
10pt; font-family: SimSun; color: windowtext;"
lang="EN-US">
<a class="moz-txt-link-abbreviated" href="mailto:gmx-users-bounces@gromacs.org">gmx-users-bounces@gromacs.org</a>
[<a class="moz-txt-link-freetext" href="mailto:gmx-users-bounces@gromacs.org">mailto:gmx-users-bounces@gromacs.org</a>] </span></font><b><font
color="black" face="宋体" size="2"><span
style="font-size: 10pt; font-family: SimSun; color:
windowtext; font-weight: bold;">代表 </span></font></b><font
color="black" face="宋体" size="2"><span style="font-size:
10pt; font-family: SimSun; color: windowtext;"
lang="EN-US">Mark Abraham<br>
</span></font><b><font color="black" face="宋体" size="2"><span
style="font-size: 10pt; font-family: SimSun; color:
windowtext; font-weight: bold;">发送时间<span
lang="EN-US">:</span></span></font></b><font
color="black" face="宋体" size="2"><span style="font-size:
10pt; font-family: SimSun; color: windowtext;"
lang="EN-US"> <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 color="black" face="宋体" size="2"><span
style="font-size: 10pt; font-family: SimSun; color:
windowtext; font-weight: bold;">收件人<span
lang="EN-US">:</span></span></font></b><font
color="black" face="宋体" size="2"><span style="font-size:
10pt; font-family: SimSun; color: windowtext;"
lang="EN-US">
Discussion list for GROMACS users<br>
</span></font><b><font color="black" face="宋体" size="2"><span
style="font-size: 10pt; font-family: SimSun; color:
windowtext; font-weight: bold;">主题<span lang="EN-US">:</span></span></font></b><font
color="black" face="宋体" size="2"><span style="font-size:
10pt; font-family: SimSun; color: windowtext;"
lang="EN-US"> Re:
[gmx-users] any software which could convert a
polypeptidesequence to a pdb
file?</span></font><font color="black" size="3"><span
style="font-size: 12pt; color: windowtext;"
lang="EN-US"><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal" style="text-align: left;" align="left"><font
color="black" face="Times New Roman" size="2"><span
style="font-size: 10.5pt;" lang="EN-US"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Times New
Roman" size="2"><span style="font-size: 10.5pt;"
lang="EN-US">On 4/20/2011 2:36 PM, Liao Chuan wrote: <o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="black" face="Arial" size="1"><span
style="font-size: 9pt; font-family: Arial;" lang="EN-US"><!--[if gte mso 9]><xml>
<u1:shapedefaults u2:ext="edit" spidmax="1026"/>
</xml><![endif]--><!--[if gte mso 9]><xml>
<u3:shapelayout u4:ext="edit">
<u3:idmap u4:ext="edit" data="1"/>
</u3:shapelayout>
</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 color="black" 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!<u5:p></u5:p></span></font><span
lang="EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-align: left;" align="left"><font
color="black" face="Times New Roman" size="3"><span
style="font-size: 12pt;" lang="EN-US"><br>
Leap in the AmberTools package is good for this.<br>
<br>
Mark<o:p></o:p></span></font></p>
</div>
</o:smarttagtype></blockquote>
<br>
</body>
</html>