[gmx-users] MARTINI simulation of protein-protein recognition

[James Starlight]

It seems like smth very complicated :)

I just need to put two different proteins in the system - one in the
membrane (A) and one in the water (B) and simulate it independently 10
times to collect statistics about associations of A and B during those
runs. The problems that I don't know how to put 2 different unbound
proteins in the MARTINI system.

James

2016-04-18 9:55 GMT+02:00 Kroon, P.C. <p.c.kroon at rug.nl>:
> Hi,
>
> I assume you want to study the binding of your water soluble protein to
> your membrane(protein). DAFT was created to do just this. DOI:
> 10.1021/ct5010092
>
> Peter
>
> On Fri, Apr 15, 2016 at 3:37 PM, James Starlight <jmsstarlight at gmail.com>
> wrote:
>
>> Dear Gromacs users!
>>
>> I am looking for some tutorial for the MARTINI simulation of
>> protein-protein recognition dealing with the big membrane protein
>> simulated within the membrane and its assosiation with the small water
>> soluble protein. The question - is it possible in existing Martini
>> system conisdted of only membrane protein solvated in membrane with
>> water to
>> i) increase box size on Z
>> ii)add some water
>> iii) put another water soluble protein in new space (on the distance
>> of the initial membrane protein complex)
>> iv) edit topology of new system and run new md
>>
>> assuming that i,ii and iv are trivial the problem here is the iii step :-)
>>
>> or alternatively if I would like to run new simulation with those 2
>> proteins (in the unbound form) how I can prepare such complex system
>> consisted of big protein in membrane plus water soluble protein
>> unbound from it?
>>
>> Thanks!
>>
>> Gleb
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