<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
On 21/11/2011 9:18 PM, archana sonawani wrote:
<blockquote
cite="mid:CAFV47mjK7e1eneyKJBjcYqjoEUKgO-+_j1_7y2=VFUH4HjHv4Q@mail.gmail.com"
type="cite">Dear Sir/Madam,
<div><br>
</div>
<div>For orienting the protein and membrane, I have used the .mdp
and following topology file:<br>
<div>
<pre style="word-wrap:break-word;white-space:pre-wrap">;
; File 'topol_popc.top' was generated
; By user: jalemkul (502)
; On host: <a moz-do-not-send="true" href="http://bevany.biochem.vt.edu" target="_blank">bevany.biochem.vt.edu</a>
; At date: Fri Oct 20 13:26:53 2006
;
; This is your topology file
;
; Include chain topologies
#include "gromos53a6_lipid.ff/forcefield.itp"
#include "popc.itp"
; Include water topology
#include "gromos53a6_lipid.ff/spc.itp"
; Include ion topologies
#include "gromos53a6_lipid.ff/ions.itp"
; System specifications
[ system ]
60-Lipid POPC Bilayer
[ molecules ]
; molecule name nr.
POPC 60
SOL 1536</pre>
<div>After running grompp to generate .tpr file I get
following error:</div>
<div><br>
</div>
<div>
<p class="MsoNormal"><span lang="EN-US"><font
color="#ff0000">Program grompp, VERSION 4.5.4</font></span></p>
<p class="MsoNormal"><span lang="EN-US"><font
color="#ff0000">Source code file: gmxcpp.c, line: 248</font></span></p>
<p class="MsoNormal"><span lang="EN-US"><font
color="#ff0000"> </font></span></p>
<p class="MsoNormal"><span lang="EN-US"><font
color="#ff0000">Fatal error:</font></span></p>
<p class="MsoNormal"><span lang="EN-US"><font
color="#ff0000">Topology include file
"gromos53a6_lipid.ff/forcefield.itp" not found</font></span></p>
<p class="MsoNormal"><span lang="EN-US"><br>
</span></p>
<p class="MsoNormal"><span lang="EN-US">But in the above
topology file, if I change the</span></p>
<p class="MsoNormal"><span lang="EN-US"><font size="4"> </font></span><span
style="font-family:monospace;white-space:pre-wrap"><font
color="#ff0000">#</font>include
"gromos53a6_lipid.ff/forcefield.itp" line to <font
color="#ff0000"><b>;</b></font></span><span
style="font-family:monospace;white-space:pre-wrap">include
"gromos53a6_lipid.ff/forcefield.itp"</span></p>
</div>
</div>
</div>
</blockquote>
<br>
This file is not optional, so failing to include anything makes
further problems. You need such a file. You are doing something
non-standard, so your burden of following directions, and/or
understanding how the include file and force field mechanism works
is a bit higher than normal :-)<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAFV47mjK7e1eneyKJBjcYqjoEUKgO-+_j1_7y2=VFUH4HjHv4Q@mail.gmail.com"
type="cite">
<div>
<div>
<div>
<p class="MsoNormal"><font face="monospace"><span
style="white-space:pre-wrap"><br>
</span></font></p>
<p class="MsoNormal"><span style="white-space:pre-wrap"><font
face="arial, helvetica, sans-serif">I get following
error:</font></span></p>
<p class="MsoNormal"><span style="white-space:pre-wrap"><font
face="arial, helvetica, sans-serif"><br>
</font></span></p>
<p class="MsoNormal"><span lang="EN-US"><font
color="#ff0000">Program grompp, VERSION 4.5.4</font></span></p>
<p class="MsoNormal"><span lang="EN-US"><font
color="#ff0000">Source code file: topio.c, line: 653</font></span></p>
<p class="MsoNormal"><span lang="EN-US"><font
color="#ff0000"> </font></span></p>
<p class="MsoNormal"><span lang="EN-US"><font
color="#ff0000">Fatal error:</font></span></p>
<p class="MsoNormal"><span lang="EN-US"><font
color="#ff0000">Syntax error - File popc.itp, line 1</font></span></p>
<p class="MsoNormal"><span lang="EN-US"><font
color="#ff0000">Last line read:</font></span></p>
<p class="MsoNormal"><span lang="EN-US"><font
color="#ff0000">'[ moleculetype ]'</font></span></p>
<p class="MsoNormal"><span lang="EN-US"><font
color="#ff0000">Invalid order for directive
moleculetype</font></span></p>
<p class="MsoNormal"><span
style="font-family:monospace;white-space:pre-wrap"><br>
</span></p>
</div>
Can anyone help me out...Thanks in adv
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
</blockquote>
<br>
</body>
</html>