[gmx-users] Membrane protein tutorial

[Justin A. Lemkul]

Pawan Kumar wrote:
> 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.
> 

What you need is a POPC_CL- group in addition to the other standard groups. 
There is a page in my tutorial (which you referenced earlier) that describes 
exactly how to do this:

http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/06_equil.html

So your index file should contain System, all the relevant protein groups, POPC, 
SOL, CL-, and SOL_CL-.  If you are considering manually modifying this file in 
some way (as I am guessing you have), don't.

-Justin

> Thanking you,
> Pawan
> 
> 
> 
> On Thu, Apr 9, 2009 at 10:14 AM, Dallas B. Warren 
> <Dallas.Warren at pharm.monash.edu.au 
> <mailto: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
>     <mailto: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>
>         [mailto: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 <mailto: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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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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