Respected Sir, Greetings from Pawan. It has worked now. I dint edit the index file before also. The problem was with the .mdp file. It was recognising lipids as POP and I gave as POPC in the .mdp file. Now there are no more errors. Thanks a lot.
Thanking you, Pawan On Thu, Apr 9, 2009 at 3:35 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Pawan Kumar wrote: > >> Hello Sir, >> >> The whole point in making an index file was to merge the sol and cl- ions. >> If i put popc also in the index file then it wont make any much useful >> group because lipids needs to be defined in a different group as I have read >> in various archives. Please do correct me if I am wrong. >> >> > What you need is a POPC_CL- group in addition to the other standard groups. > There is a page in my tutorial (which you referenced earlier) that describes > exactly how to do this: > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/06_equil.html > > So your index file should contain System, all the relevant protein groups, > POPC, SOL, CL-, and SOL_CL-. If you are considering manually modifying this > file in some way (as I am guessing you have), don't. > > -Justin > > Thanking you, >> Pawan >> >> >> >> On Thu, Apr 9, 2009 at 10:14 AM, Dallas B. Warren < >> dallas.war...@pharm.monash.edu.au <mailto: >> dallas.war...@pharm.monash.edu.au>> wrote: >> >> Well, as the error says, popc isn't defined in the index file. Seems >> grompp is looking for a popc entry in the index file, and >> can't find it. So, I would hazard to say, you need to define it. >> Catch ya, >> >> Dr. Dallas Warren >> Department of Pharmaceutical Biology and Pharmacology >> Pharmacy and Pharmaceutical Sciences, Monash University >> 381 Royal Parade, Parkville VIC 3010 >> dallas.war...@pharm.monash.edu.au >> <mailto:dallas.war...@pharm.monash.edu.au> >> +61 3 9903 9167 >> --------------------------------- >> When the only tool you own is a hammer, every problem begins to >> resemble a nail. >> >> >> ------------------------------------------------------------------------ >> *From:* gmx-users-boun...@gromacs.org >> <mailto:gmx-users-boun...@gromacs.org> >> [mailto:gmx-users-boun...@gromacs.org >> <mailto:gmx-users-boun...@gromacs.org>] *On Behalf Of *Pawan Kumar >> *Sent:* Thursday, 9 April 2009 2:39 PM >> *To:* jalem...@vt.edu <mailto:jalem...@vt.edu>; Discussion list >> >> for GROMACS users >> *Subject:* Re: [gmx-users] Membrane protein tutorial >> >> Hello sir, >> >> Thanks for such a explanatory tutorial. >> I am stuck with one error now. >> I have protein, popc, sol and cl- in my system. >> I have merged the sol and cl- using make_ndx. >> But when I run grompp I get the error like this "popc not >> defined in the index file". >> The grompp command : grompp -f pr.mdp -c box_em.pdb -p topol.top >> -o box_pr.tpr >> Any suggestions please. >> * >> pr.mdp file :* >> title = protein in popc bilayer >> cpp = /usr/bin/cpp >> define = -DPOSRES -DPOSRES_LIPID >> constraints = all-bonds >> constraint-algorithm= Lincs >> integrator = md >> dt = 0.002 nsteps = 5000 >> nstcomm = 1 >> nstxout = 50 >> nstvout = 1000 >> nstfout = 0 >> nstlog = 10 >> nstenergy = 10 >> nstlist = 10 >> ns_type = grid >> rlist = 1 >> coulombtype = PME >> rcoulomb = 1 >> vdw-type = Cut-off >> rvdw = 1 >> ; Berendsen temperature coupling is on in two groups >> tcoupl = berendsen >> tc_grps = Protein POPC SOL_CL- >> tau_t = 0.1 0.1 0.1 >> ref_t = 300 300 300 >> ; Energy monitoring >> energygrps = Protein POPC SOL_CL- >> ; Pressure coupling is on >> ;Pcoupl = berendsen >> tau_p = 2.0 2.0 >> compressibility = 4.5e-5 4.5e-5 >> ref_p = 1.0 1.0 >> Pcoupl_type = semiisotropic >> ; Generate velocites is on at 300 K. >> gen_vel = yes >> gen_temp = 300.0 >> gen_seed = 173529 >> >> Thanking you, >> Pawan >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php