[gmx-users] Membrane protein tutorial
pawan.chinari at gmail.com
Thu Apr 9 06:55:08 CEST 2009
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.
On Thu, Apr 9, 2009 at 10:14 AM, Dallas B. Warren <
Dallas.Warren at 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.warren at pharm.monash.edu.au
> +61 3 9903 9167
> When the only tool you own is a hammer, every problem begins to resemble a
> *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
> 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
> 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,
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