[gmx-users] Membrane protein tutorial
Pawan Kumar
pawan.chinari at gmail.com
Thu Apr 9 12:21:51 CEST 2009
Respected Sir,
Greetings from Pawan.
It has worked now.
I dint edit the index file before also. The problem was with the .mdp file.
It was recognising lipids as POP and I gave as POPC in the .mdp file. Now
there are no more errors.
Thanks a lot.
Thanking you,
Pawan
On Thu, Apr 9, 2009 at 3:35 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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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