[gmx-users] Membrane protein tutorial
Dallas B. Warren
Dallas.Warren at pharm.monash.edu.au
Thu Apr 9 06:44:25 CEST 2009
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.
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
When the only tool you own is a hammer, every problem begins to resemble
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Pawan Kumar
Sent: Thursday, 9 April 2009 2:39 PM
To: jalemkul at vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Membrane protein tutorial
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
Any suggestions please.
pr.mdp file :
title = protein in popc bilayer
cpp = /usr/bin/cpp
define = -DPOSRES -DPOSRES_LIPID
constraints = all-bonds
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
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users