[gmx-users] MARTINI simulation of protein-protein recognition
Smith, Micholas D.
smithmd at ornl.gov
Mon Apr 18 15:51:14 CEST 2016
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 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.
2016-04-18 9:55 GMT+02:00 Kroon, P.C. <p.c.kroon at rug.nl>:
> 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:
> On Fri, Apr 15, 2016 at 3:37 PM, James Starlight <jmsstarlight at gmail.com>
>> 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?
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