Will you please send me the basic tutorial in which I can find how to use -n option in " grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr" command.<br><br><div class="gmail_quote">On Mon, Feb 6, 2012 at 5:17 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im"><br>
<br>
Anushree Tripathi wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
where should I use -n option in the command (i.e., grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr).Please tell me.<br>
<br>
</blockquote>
<br></div>
I would suggest you refer to grompp -h and/or go through some basic tutorial material so that you can get a feel for command line options and how to apply them.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im">
On Mon, Feb 6, 2012 at 4:58 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.<u></u>au</a>>> wrote:<br>
<br>
On 6/02/2012 8:28 PM, Anushree Tripathi wrote:<br>
<br>
Inspite of having DPPC in index file,when I run the command (<br>
i.e., grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr ),I am<br>
getting the error:<br>
<br>
Group DPPC not found in indexfile.<br>
Maybe you have non-default goups in your .mdp file, while not<br>
using the '-n' option of grompp.<br>
In that case use the '-n' option.<br>
<br>
Now, what to do? Please guide me.<br>
<br>
<br>
You seem not to have used the -n option. You could try using it. :)<br>
<br>
Mark<br>
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Justin A. Lemkul<br>
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Department of Biochemistry<br>
Virginia Tech<br>
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