<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 05/11/2011 06:24 AM, Frank Neuhaus wrote:
<blockquote
cite="mid:20110510202426.A47F976E1F@mailp1.ci.northwestern.edu"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta content="MSHTML 6.00.6000.17097" name="GENERATOR">
<div><font face="Arial" size="2"><span class="890210920-10052011">Hi,</span></font></div>
<div><font face="Arial" size="2"><span class="890210920-10052011"></span></font> </div>
<div><font face="Arial" size="2"><span class="890210920-10052011">I
have a protein simulation in which all residues simulate
correctly with the exception of five in a loop. These five
out of 360 are in a loop (or bend) separate from my area of
interest. Thus, I would like to treat them as a rigid
sequence. Using the position restraints in the posre.itp
file does not help me. I am looking for a script that I can
write into my mdp files that restricts all simulation in
these five residues. Can anyone help me with this little
issue? Thank you.</span></font></div>
</blockquote>
<br>
What about their motion is not "correct"? If this is a disordered
loop, then probably your reference data for these residues is less
reliable than the MD simulation ensemble.<br>
<br>
Mark<br>
</body>
</html>