<div dir="ltr">my command was:<br><br>/share/apps/gromacs-4.5.2/bin/grompp_mpi -f md.mdp -c ../../membed_17_npt.gro.884814.gro -t ../../membed_17_npt.trr.884814.trr -e ../../membed_17_npt.edr.884814.edr -p topol_protein_dppc_sol3_22.top -n index.ndx -o md_0_1_22.tpr<br>
<br>the name of the edr file (and other NPT outputs) is because i'm running it in qsub and therefore it contains the job id... that's all.<br><br>Do you have any solution?<br><br>Thanks,<br>Adva<br><br><div class="gmail_quote">
On Mon, Nov 22, 2010 at 2:10 PM, 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 text="#000000" bgcolor="#ffffff"><div class="im">
On 22/11/2010 11:03 PM, Adva Suez wrote:
<blockquote type="cite">
<div dir="ltr">Hello,<br>
I'm using your KALP in DPPC tutorial to figure out how to
simulate a molecule in a membrane in GROMACS. I'm using version
4.5.2 and
from some reason I got an error in grompp whe trying generate
md_0_1.tpr.
<br>
the error is: <br>
<br>
Program grompp_mpi, VERSION 4.5.2<br>
Source code file: enxio.c, line: 1097<br>
<br>
Fatal error:<br>
Could not find frame with time 1000.000061 in
'../../membed_17_npt.edr.884814.edr'<br>
</div>
</blockquote>
<br></div>
That's a seriously weird .edr file name. What was your command line?<br><font color="#888888">
<br>
Mark</font><div class="im"><br>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">
<br>
This is weird because I only have 1000 frames in the NPT
run...<br>
Can you please help me?<br>
<br>
Thanks,<br>
Adva.</div>
<br clear="all">
<br>
-- <br>
<div dir="ltr"><font face="arial, helvetica, sans-serif">Adva
Yeheskel<br>
Bioinformatics Unit<br>
Rm 001, Sherman bldg.,<br>
G.S.W. Faculty of Life Sciences<br>
Tel-Aviv University, ISRAEL 69978 <br>
<br>
Tel: 972-3-6406840; Fax: 972-3-6405098<br>
E-mail: </font><a href="mailto:suezadva@tauex.tau.ac.il" target="_blank"><font face="arial, helvetica, sans-serif">suezadva@tauex.tau.ac.il</font></a><font face="arial, helvetica, sans-serif"><br>
Web-site: </font>
<div style="display: inline;"><span style="border-collapse: collapse;"><a href="http://www.tau.ac.il/lifesci/bioinformatics.html" style="color: rgb(28, 81, 168);" target="_blank"><font face="arial, helvetica, sans-serif">http://www.tau.ac.il/lifesci/</font><font face="arial, helvetica, sans-serif">bioinformatics.html</font></a></span></div>
</div>
<br>
</div>
</blockquote>
<br>
</div></div>
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Bioinformatics Unit<br>Rm 001, Sherman bldg.,<br> G.S.W. Faculty of Life Sciences<br> Tel-Aviv University, ISRAEL 69978 <br> <br> Tel: 972-3-6406840; Fax: 972-3-6405098<br> E-mail: </font><a href="mailto:suezadva@tauex.tau.ac.il" target="_blank"><font face="arial, helvetica, sans-serif">suezadva@tauex.tau.ac.il</font></a><font face="arial, helvetica, sans-serif"><br>
Web-site: </font><div style="display: inline;"><span style="border-collapse: collapse;"><a href="http://www.tau.ac.il/lifesci/bioinformatics.html" style="color: rgb(28, 81, 168);" target="_blank"><font face="arial, helvetica, sans-serif">http://www.tau.ac.il/lifesci/</font><font face="arial, helvetica, sans-serif">bioinformatics.html</font></a></span></div>
</div><br>
</div>