Hi Jestin,<br><br>Read chapter 5 thoroughly :)<br>It seems that in your topology file (minding the #includes) the directive [ system ] is given too early, e.g. before the definition of the [ moleculetypes ].<br><br>Tsjerk<br>
<br><div class="gmail_quote">On 25 Nov 2007 05:51:50 -0000, JMandumpal <<a href="mailto:jesbman@rediffmail.com">jesbman@rediffmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<p>
Dear Gromacs users,<br>
<br>
When I tried to build up .tpr file for running energy minimisation, I encountered some problems:<br>
<br>
This is the command I used:<br>
<br>
<br>
grompp -f em.mdp -p topol.top -c out.gro -o pr.tpr<br>
<br>
<br>
and I received the following error message:<br>
<br>
Fatal error:<br>
Invalid order for directive system, file ""topol.top"", line 4<br>
-------------------------------------------------------<br>
<br>
<br>
How can I solve this?<br>
<br>
<br>
regards,<br>
Jestin Mandumpal<br>
</p>
<br><br>
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</a><br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8 <br>3584 CH Utrecht<br>The Netherlands<br>
P: +31-30-2539931 <br>F: +31-30-2537623