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
