[gmx-users] MD with membrane protein

[elisa carli]

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?

Bests

2011/9/22 lina <lina.lastname at gmail.com>

>  On Thu, Sep 22, 2011 at 11:34 AM, elisa carli <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
>
> mdrun_g -v -deffnm em
>
> works well.
>
>
> --
> Best Regards,
>
> lina
>
>
>
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