<!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 bgcolor="#ffffff" text="#000000">
<div bidimailui-direction-uniformity="ltr" dir="ltr"
style="direction: ltr;" bidimailui-generated="true">Thanks Mark
for the replay,
</div>
<div bidimailui-direction-uniformity="neutral"
bidimailui-generated="true">
</div>
<br>
<div bidimailui-direction-uniformity="ltr" dir="ltr"
style="direction: ltr;" bidimailui-generated="true">I used VDW
presentation to over come it.
</div>
<div bidimailui-direction-uniformity="neutral"
bidimailui-generated="true">
</div>
<br>
<div bidimailui-direction-uniformity="ltr" dir="ltr"
style="direction: ltr;" bidimailui-generated="true">Best,
</div>
<div bidimailui-direction-uniformity="ltr" dir="ltr"
style="direction: ltr;" bidimailui-generated="true">Itamar
</div>
<br>
<br>
On 6/09/2010 6:33 PM, Mark Abraham wrote:
<blockquote cite="mid:fbb28bd8118d5.4c8533dc@anu.edu.au" type="cite"><br>
<br>
----- Original Message -----<br>
From: Itamar Kass <a class="moz-txt-link-rfc2396E" href="mailto:itamar.kass@monash.edu"><itamar.kass@monash.edu></a><br>
Date: Monday, September 6, 2010 14:06<br>
Subject: [gmx-users] Protein stability using MARTINI<br>
To: Discussion list for GROMACS users
<a class="moz-txt-link-rfc2396E" href="mailto:gmx-users@gromacs.org"><gmx-users@gromacs.org></a><br>
<br>
> HI all,<br>
> <br>
> I am simulating a protein in water using the MARTINI (CG)
force <br>
> field. My protein composed of few alpha-helices and a big
tail <br>
> (~50AA) which is random coiled. I have built the simulation <br>
> system according to the procedure at <br>
>
<a class="moz-txt-link-freetext" href="http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in">http://md.chem.rug.nl/cgmartini/index.php/tutorial/ubiquitin-in</a>-<br>
> water .<br>
> <br>
> After a 10ns simulation, I have visualised the system using
VMD. <br>
> It seems like the protein had dismantled to amino acids. I
see <br>
> groups of bids moving freely in the system.<br>
<br>
I'm not sure what you mean here, but it seems likely that VMD's
heuristics for guessing where bonds between atoms might exist
aren't going to work well for a coarse-grained protein. There's
probably a standard solution, for which you should Google :-)<br>
<br>
Mark<br>
<br>
> <br>
> Any idea of the problem? Any idea how to fix it?<br>
> <br>
> PS I don't want to use elastic network for the random coil
tail, <br>
> as I wish to capture as much conformation as possible.<br>
> <br>
> Thanks in advance,<br>
> Itamar.<br>
> <br>
> -- <br>
> <br>
> <br>
> "In theory, there is no difference between theory and
practice. <br>
> But, in practice, there is." - Jan L.A. van de Snepscheut<br>
> <br>
> ===========================================<br>
> | Itamar Kass, Ph.D.<br>
> | Postdoctoral Research Fellow<br>
> |<br>
> | Department of Biochemistry and Molecular Biology<br>
> | Building 77 Clayton Campus<br>
> | Wellington Road<br>
> | Monash University,<br>
> | Victoria 3800<br>
> | Australia<br>
> |<br>
> | Tel: +61 3 9902 9376<br>
> | Fax: +61 3 9902 9500<br>
> | E-mail: <a class="moz-txt-link-abbreviated" href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a><br>
> ============================================<br>
> <br>
> -- <br>
> gmx-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a class="moz-txt-link-freetext" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
> Please search the archive at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> <br>
> before posting!<br>
> Please don't post (un)subscribe requests to the list. Use the
<br>
> www interface or send it to <a class="moz-txt-link-abbreviated" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>
> Can't post? Read
<a class="moz-txt-link-freetext" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
"In theory, there is no difference between theory and practice. But, in practice, there is." - Jan L.A. van de Snepscheut
===========================================
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: <a class="moz-txt-link-abbreviated" href="mailto:Itamar.Kass@monash.edu">Itamar.Kass@monash.edu</a>
============================================
</pre>
</body>
</html>