[gmx-users] MD with membrane protein

[lina]

On Tue, Oct 4, 2011 at 2:57 AM, elisa carli <elisacarli21 at gmail.com> 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?
>
Yes, after energy minimization, you need do some other sets (like NVT and
NPT).

Could you write me which are the commands to execute up to MD run?
>

The links Justin provided are very useful. It's not a bad idea to do some
tutor to be familiar with those procedures.


>
> 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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>
>
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-- 
Best Regards,

lina
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