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.
Thanking you, Pawan On Thu, Apr 9, 2009 at 10:14 AM, Dallas B. Warren < [email protected]> 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 > [email protected] > +61 3 9903 9167 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > ------------------------------ > *From:* [email protected] [mailto: > [email protected]] *On Behalf Of *Pawan Kumar > *Sent:* Thursday, 9 April 2009 2:39 PM > *To:* [email protected]; 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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