[gmx-users] Membrane protein tutorial

[Pawan Kumar]

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 <
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
> nail.
>
>
>  ------------------------------
> *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
> 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
>
>
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