Hi Ashutosh,<br>
<br>
If no index file is explicitly given to grompp, it will use default
index group (as if you did echo q | make_ndx -f test_b4pr.gro -o
index.ndx) Grompp does not know of definitions given in the .top file
with regards to the groups. Does your protein contain some non-standard
residues? Try to explicitly create an index file and see if the groups
"Protein" and "SOL" cover all atoms in your system. ( N(Proteins) +
N(SOL) = N(System) ). If not, make adjustments to the index file by
merging appropriate groups, i.e. merge non-standard protein groups with
the protein if necessary. Note that this basically was the problem
given in the last post about "Not enough ref_t and tau_t values".<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<br><br><div><span class="gmail_quote">On 3/16/06, <b class="gmail_sendername">X.Periole</b> <<a href="mailto:X.Periole@rug.nl">X.Periole@rug.nl</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
On Wed, 15 Mar 2006 17:21:52 -0600<br> Ashutosh Jogalekar <<a href="mailto:ajogale@emory.edu">ajogale@emory.edu</a>> wrote:<br>> I know this question has been discussed a number of<br>>times on the list, but almost everytime it has been
<br>>discussed in reference to the index file.<br>> I am getting this error during grompp for the position<br>>restrained MD even though I am not using any index file.<br>>The only groups I have are solvent and protein and
<br>>accordingly, there are two columns for these two in the<br>>tau_t and ref_t fields in the pr.mdp file:<br>><br>> tau_t= 0.1 0.1<br>> tc_grps= protein sol<br>> ref_t= 300 300
<br>><br>> my command is:<br>><br>> grompp -f pr.mdp -c test_b4pr.gro -p test.top -o<br>>test_em.tpr<br>><br>> In spite of this, the error is showing up again and<br>>again. The top file also has a row only for protein and
<br>>solvent.<br><br>If all the atoms of your protein or solvent are not<br>included<br>in the indexes defined by default (protein sol) I think<br>grompp find them out of any index and then looks for more<br>tau_t and ref_t ... I would check the topology of your
<br>system. It might be uncorrect.<br><br>XAvier<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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Groningen Biomolecular Sciences and Biotechnology Institute (GBB)<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336<br>