[gmx-users] MD with membrane protein

[Justin A. Lemkul]

elisa carli wrote:
> Hi Lisa
>  
> Thank you very much for your reply.
> After minimimization could I run a molecular dynamic production?
> Or have I to do other sets?
> Could you write me which are the commands to execute up to MD run?
>  

http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation

There is also a membrane protein tutorial linked from

http://www.gromacs.org/Documentation/Tutorials

The approach is slightly different from what has been posted before, but perhaps 
it will be of some use.

-Justin

> Bests
> 
> 2011/9/22 lina <lina.lastname at gmail.com <mailto:lina.lastname at gmail.com>>
> 
>     On Thu, Sep 22, 2011 at 11:34 AM, elisa carli
>     <elisacarli21 at gmail.com <mailto:elisacarli21 at gmail.com>> wrote:
> 
>         Dear All
>          
>         I'd like to perfom a MD simulation on a membrane protein using
>         DLPC or DPPC system
>         I've downloaded the API package from this link
>         http://www.gromacs.org/Downloads/User_contributions/Molecule_topologies
>          
>         DPPC.zip and DLPC.zip by schiu
>          
>         How can I use them? Where can I get a tutorial or commands
>         illustrating the use of these packages?
>          
>         Thanks in advance
> 
>      Here is a rough procedure:
> 
>     http://www.nanoconductor.org/43A1-S3/
> 
>     Took Chiu's  DPPC.zip as an example. We use the speptide.pdb peptide
>     from the gromacs tutorial (it's a bad choice to put it in the dppc,
>     but we just try it).
> 
>     pdb2gmx_g -f speptide.pdb -o speptide.gro
> 
>     choose
>     9: GROMOS96 43a1 force field
>     1: SPC    simple point charge, recommended
> 
>     $ tail -1 dppc.gro
>        5.68585   5.60685   6.85739
> 
>     To be as simple as possible here, we use the dimension of the dppc.gro
> 
>     editconf_g -f speptide.gro -o speptide_newbox.gro -center 2.5 2.5
>     4.2  -box  5.68585   5.60685   6.85739
>      
>     now solvate the peptide into the pre-equilibrillium-ed DPPC.gro by
> 
>     genbox_g -cp speptide_newbox.gro -cs dppc.gro -o system.gro -p topol.top
> 
> 
>     Now cp the em.mdp from some_path_to/share/gromacs/tutor/speptide,
> 
>     the purpose of doing a simple energy minimization here just want to
>     "test" the topol.top.
> 
>     it used 43A1-S3 force field (You can download from
>     http://www.nanoconductor.org/43A1-S3/).
> 
>     The head of topol.top:
>     ; Include forcefield parameters
>     #include "ffG43A1-S3.itp"
>     #include "lipids_43A1-S3.itp"
> 
>     The tail of topol.top:
> 
>     [ molecules ]
>     ; Compound        #mols
>     Protein             1
>     DPPC         71
>     SOL              3205
> 
>     I manually added DPPC  71.
> 
>     please copy the  lipids_43A1-S3.itp    ffG43A1-S3.itp   
>     ffG43A1-S3par.02.itp from the downloaded 43A1-S3 force field into
>     current directory,
>     extra copy ff_dum.itp from 
>     some_path_to/share/gromacs/top/43a1s3.ff/ff_dum.itp into current
>     working directory.
> 
>     I attached all those files in try.tar.gz
>     https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB
>     <https://docs.google.com/leaf?id=0B93SVRfpVVg3ZmUxM2ExOTctYTJlNC00MzAxLWI4ZWItNDI2MGM4OThmN2Nj&hl=en_GB>
> 
>     mdrun_g -v -deffnm em
> 
>     works well.
> 
> 
>     -- 
>     Best Regards,
> 
>     lina
> 
> 
> 
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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