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

[James Starlight]

Ok thanks I will look into the tutorial!

J.

2016-04-18 16:02 GMT+02:00 Kroon, P.C. <p.c.kroon at rug.nl>:
> @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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