<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#ffffff">
On 30/06/2011 1:48 PM, rashi parihar wrote:
<blockquote
cite="mid:BANLkTinFkHWe=wV-LHE+m+DpmDAG2C0Cjw@mail.gmail.com"
type="cite">thanx @justin..I have seen gromacs web site before
posting..the solution of my problem was written in gromacs website
was "<span style="color: rgb(204, 0, 0);"> the atom names are
expected to match those found in the </span><a
moz-do-not-send="true" style="color: rgb(204, 0, 0);"
title="Documentation/File Formats/.rtp File" rel="internal"
href="http://www.gromacs.org/Documentation/File_Formats/.rtp_File">.rtp
file</a><span style="color: rgb(204, 0, 0);"> that define the
building block(s) in your structure"</span>. Now my question is
that how can i see or open the .rtp file of particular force
field?<br style="color: rgb(204, 0, 0);">
</blockquote>
<br>
Yes, it's somewhere under share/top of your GROMACS installation
directory - and probably pdb2gmx prints which one it is trying to
use.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTinFkHWe=wV-LHE+m+DpmDAG2C0Cjw@mail.gmail.com"
type="cite">
<br>
<div class="gmail_quote">On Wed, Jun 29, 2011 at 5:24 PM, Justin
A. Lemkul <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div class="im"><br>
<br>
rashi parihar wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
HI all ..while running pdb2gmx command .I am getting error
"Fatal error:<br>
Atom CT in residue TYR 314 was not found in rtp entry TYR
with 20 atoms<br>
while sorting atoms" .what this error mean and how can I
rectify this problem?plz help me.<br>
</blockquote>
<br>
</div>
Please search the mailing list archive and Gromacs website
before posting. Nearly all common errors are explained on the
website or within a few seconds of searching. For instance:<br>
<br>
<a moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry"
target="_blank">http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
-- <br>
<div class="im">
images[12]<br>
“Many Smiles Begin Because Of Another Smile . . . ."<br>
Regards,<br>
Rashi<br>
<br>
</div>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a moz-do-not-send="true" href="http://vt.edu"
target="_blank">vt.edu</a> | (540) 231-9080<br>
<a moz-do-not-send="true"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
<font color="#888888">
-- <br>
gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists/Search"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
Please don't post (un)subscribe requests to the list. Use
the www interface or send it to <a moz-do-not-send="true"
href="mailto:gmx-users-request@gromacs.org"
target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a moz-do-not-send="true"
href="http://www.gromacs.org/Support/Mailing_Lists"
target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
<div> </div>
<div><span style="font-size: 24pt; color: rgb(255, 102, 0);
font-family: Wingdings;"><img alt="images[12]"
src="cid:part1.06060405.09090802@anu.edu.au" width="99"
height="106"></span></div>
<div> </div>
<div>“Many Smiles Begin Because Of Another Smile . . . ." <br>
<br>
Regards,<br>
Rashi</div>
<br>
</blockquote>
<br>
</body>
</html>