Hello Mark Sir,<br><br>I have tried that way also.<br>The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p topol.top -o box_pr.tpr<br>But this time i get an error like this "Atom 1 defined in multiple groups (1 & 3). "<br>
How to overcome this error ?<br><br>Thanking you,<br>Pawan<br><br><div class="gmail_quote">On Thu, Apr 9, 2009 at 10:14 AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">Pawan Kumar wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Hello sir,<br>
<br>
Thanks for such a explanatory tutorial.<br>
I am stuck with one error now.<br>
I have protein, popc, sol and cl- in my system.<br>
I have merged the sol and cl- using make_ndx.<br>
But when I run grompp I get the error like this "popc not defined in the index file".<br>
The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top -o box_pr.tpr<br>
</blockquote>
<br></div>
As I said last time, you'll need to give grompp the index file so that it can make sense of your use of the new group(s) name(s).<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
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