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

[Kroon, P.C.]

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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