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 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>
<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"></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></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>