[gmx-users] Membrane protein tutorial

[Mark Abraham]

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.

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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