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

[Kroon, P.C.]

@Michael: Yes, you are right, a protein is a protein. IIRC the martinize
script does the same as pdb2gmx in this case.
@James: It really sounds like you want to do DAFT.
http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/downloads/DAFT/index.shtml
seems to contain an tutorial. Otherwise, consider contacting the author of
the paper (T Wassenaar).

Peter

On Mon, Apr 18, 2016 at 3:51 PM, Smith, Micholas D. <smithmd at ornl.gov>
wrote:

> Hi James,
>
> My guess is that running a two (unbound) protein simulation with the
> MARTINI force-field will be the same as if it was all atom. Build two
> separate protein topologies (with Martini force-fields) as *.itp files to
> include in your *.top and go from there. The topology file is what grompp
> uses to determine bonding, so if the topology file doesn't have the two
> proteins bound, they won't be. If I remember correctly, you can see an
> example (all-atom) topology file to work with if you use pdb2gmx for a pdb
> that contains 2 chains (with the proper flag the chains will be split).
>
> -Micholas
>
> ===================
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
>
> ________________________________________
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of James
> Starlight <jmsstarlight at gmail.com>
> Sent: Monday, April 18, 2016 9:43 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] MARTINI simulation of protein-protein recognition
>
> 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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