Thanks for the response Tsjerk ! I'm sorry that i haven't included any information in my prev post.<br>here's my mdp file.<br><br>;<br>; User spoel (236)<br>; Wed Nov 3 17:12:44 1993<br>; Input file
<br>;<br>title = Yo<br>cpp = /usr/bin/cpp<br>constraints = all-bonds<br>integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 5000 ; total 10 ps.
<br>nstcomm = 1<br>nstxout = 250<br>nstvout = 1000<br>nstfout = 0<br>nstlog = 100<br>nstenergy = 100<br>nstlist = 10<br>ns_type = grid
<br>rlist = 1.0<br>rcoulomb = 1.0<br>rvdw = 1.0<br>; Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>tc-grps = Protein SOL Cl
<br>tau_t = 0.1 0.1 0.1<br>ref_t = 300 300 300<br>; Energy monitoring<br>energygrps = Protein SOL Cl Protein_MET_1<br>energygrps_excl = Protein Protein SOL SOL
<br>; Isotropic pressure coupling is now on<br>Pcoupl = berendsen<br>Pcoupltype = isotropic<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>; Generate velocites is off at 300 K.
<br>gen_vel = no<br>gen_temp = 300.0<br>gen_seed = 173529<br><br>i had added the groups to the energy monitoring section of the mdp file. and the error generated was<br><br>Program grompp, VERSION
3.3<br>Source code file: readir.c, line: 819<br><br>Fatal error:<br>Atom 1 in multiple Energy Mon. groups (1 and 4)<br><br>Thanks for your help !<br>regards,<br>Kota.<br><br><div><span class="gmail_quote">On 5/1/07, <b class="gmail_sendername">
Tsjerk Wassenaar</b> <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</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;">
Hi Kota,<br><br>In your .mdp file, under energy_grps, you should list your residues.<br>As you didn't give much more information, it's hard to tell why grompp<br>bailed out. The error message is usually a good thing to add to a
<br>mail, and in this case, the .mdp file might be too.<br><br>Cheers,<br><br>Tsjerk<br><br>On 5/1/07, Pradeep Kota <<a href="mailto:kotanmd@gmail.com">kotanmd@gmail.com</a>> wrote:<br>> Dear users,<br>><br>> I'm trying to compute the contribution of each residue to the total energy
<br>> of a protein. I neutralized my system with 8 chloride ions and then made an<br>> index file with each residue in a different index group, using 'splitres'<br>> via make_ndx. it gave me an index file with atoms of each residue in
<br>> different index groups. but as all these atoms are again listed in the<br>> default index group - Protein, grompp shouts out a fatal error. there was a<br>> post on the list about index groups being bungled up after taking the system
<br>> thro genion. but i dont think genion really matters in my case. any inputs?<br>> my idea is to calculate the energy of each residue in a given protein. i<br>> wish to run a simulation for 10 ps for that. am i going wrong anywhere? is
<br>> there a better way?<br>><br>> thanks in advance<br>> Kota.<br>><br>> _______________________________________________<br>> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org
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<br>> <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br>><br><br><br>--<br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center
<br>Utrecht University<br>Padualaan 8<br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931<br>F: +31-30-2537623<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">
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<a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></blockquote></div><br>