<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; ">Thanks Tsjerk<DIV>Yes, there was a non-standard amino acid residue and it was not recognising it as part of the protein. I changed the total number of residues in the aminoacid.dat file (which I had not!) and then everything worked ok.</DIV><DIV>Ashutosh</DIV><DIV><BR><DIV><DIV>On Mar 16, 2006, at 3:09 AM, Tsjerk Wassenaar wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite">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"> http://www.gromacs.org/mailman/listinfo/gmx-users</A><BR>Please don't post (un)subscribe requests to the list. Use the<BR>www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org </A>.<BR>Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A><BR></BLOCKQUOTE></DIV><BR><BR clear="all"><BR>-- <BR><BR>Tsjerk A. Wassenaar, M.Sc.<BR> 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><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE></DIV><BR></DIV></BODY></HTML>