[gmx-users] Membrane protein tutorial
Justin A. Lemkul
jalemkul at vt.edu
Thu Apr 9 17:39:21 CEST 2009
Mark Abraham wrote:
> Justin A. Lemkul 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:
>
> A new SOL_CL- group is what is needed, not POPC_CL-, probably a typo.
>
Oops, indeed :)
-Justin
> Mark
>
>> 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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