<html>
<head>
<meta content="text/html; charset=UTF-8" http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<br>
<blockquote
cite="mid:OJFYXTZTARSGPGLLQEROCODNOYFS.20104227043@suda.edu.cn"
type="cite">
<div>Here is the detailed info about my setup:</div>
<div>System:64-bit Linux</div>
<div>GMX version:4.5.4</div>
<div>I know that windows and linux have different line end format
and I didn't edit my text files using editor on windows,but all
on linux.</div>
</blockquote>
Which editor? Problems in principle could arise from your encodings
setup, even on linux.<br>
<br>
<blockquote
cite="mid:OJFYXTZTARSGPGLLQEROCODNOYFS.20104227043@suda.edu.cn"
type="cite">
<div>My goal is to simulate membrane protein embeded in lipid
bilayer,I don't have experience working with gromacs before,so I
followed the tutorial recommended by the official gromacs
website:</div>
<div><a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html</a></div>
<div>I downloaded the files offered by the tutorial and proceeded
and then encountered some problems.</div>
<div>As there is no lipid molecular defenition in gromacs,the
tutorial refered me to this link:</div>
<div><a moz-do-not-send="true"
href="http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies">http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies</a></div>
<div>to download the so called "Berger lipids",I did exactly what
the tutorial instucted.</div>
<div>When I called pdb2gmx,I found the nomenclature of atoms in
"Berger lipids" is not consistent with that of the gromos53a6
forcefield.</div>
<div>I abandoned "Berger lipids" because I found the DPPC lipid
model offered by Oxford lipidbook is consistent with gromos53a6
forcefield,then pdb2gmx worked.You can find the lipidbook here:</div>
<div><a moz-do-not-send="true"
href="http://lipidbook.bioch.ox.ac.uk/package/show/id/14.html">http://lipidbook.bioch.ox.ac.uk/package/show/id/14.html</a></div>
<div>After generating the .gro file,I called grompp to generate
the .tpr file,and then,grompp throwed the very error message in
my original mail.I didn't modify the files generated by the
programs I called.</div>
<div>In order to re-generate the error message, I zipped the
forcefield files I used, you can find it here:</div>
<div><a moz-do-not-send="true"
href="http://ishare.iask.sina.com.cn/f/21401866.html?w=%27%20target=%27_blank%27">http://ishare.iask.sina.com.cn/f/21401866.html?w='%20target='_blank'</a></div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Grenoble
_________________________________________________________
Please avoid sending me Word or PowerPoint attachments.
See <a class="moz-txt-link-freetext" href="http://www.gnu.org/philosophy/no-word-attachments.html">http://www.gnu.org/philosophy/no-word-attachments.html</a></pre>
</body>
</html>