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

jkrieger at mrc-lmb.cam.ac.uk jkrieger at mrc-lmb.cam.ac.uk
Tue Apr 19 15:55:03 CEST 2016 

How about aligning the original MEMBRANEsystem.gro and waterSOLprot.gro
onto the relevant part of solvatedNEW.gro in pymol (after converting to
PDB) and then creating and saving a new object from both parts which you
use as input for pdb2gmx to create the topology. That way both parts have
their original residue orders.

> a now I understand that genbox has reorented the order the residues in
> the protein which was embedded in the membrane used as the solvent >)
>
> is it possible to prevent the order of all residues in the system
> provided by -cs flag?
>
> 2016-04-19 15:14 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
>> btw I have tried to insert second molecular using just genbox having
>> both components oriented properly in the space before
>>
>> g_genbox -cp waterSOLprot.gro -cs MEMBRANEsystem.gro -vdwd 0.21 -o
>> solvatedNEW.gro -box 18 18 28
>>
>> than checking VMD solvatedNEW.gro - everything was looks perfect- the
>> waterSOLprot has been placed in proper position and overlapped CG
>> water has been removed.
>>
>> now running gromppt I received
>>
>> WARNING 1 [file system.top, line 49]:
>>   2886 non-matching atom names
>>   atom names from system.top will be used
>>   atom names from system.gro will be ignored
>>
>>
>> I also should specify that after genbox I edited new topology.top
>> manually
>> putting chains of the proteins in correct order (like in new gro file
>> produced by genbox) and putting correct number of W
>>
>> assuming that initially I have multi chain protein in the POPC membrane
>> and using genbox I added to the system one new chain Z
>>
>> before
>> [quote]Protein_A      1
>> Protein_B      1
>> Protein_C      1
>> Protein_D      1
>> Protein_E      1
>> Protein_F      1
>> Protein_G      1
>> Protein_H      1
>> Protein_I      1
>> Protein_J      1
>> Protein_K      1
>> Protein_L      1
>> Protein_M      1
>> POPC           451
>> CHOL             0
>> POPC           451
>> CHOL             0
>> W            61226
>> NA+            678
>> CL-            671[/quote]
>>
>> after
>> [quote]Protein_Z      1
>> Protein_A      1
>> Protein_B      1
>> Protein_C      1
>> Protein_D      1
>> Protein_E      1
>> Protein_F      1
>> Protein_G      1
>> Protein_H      1
>> Protein_I      1
>> Protein_J      1
>> Protein_K      1
>> Protein_L      1
>> Protein_M      1
>> POPC           451
>> CHOL             0
>> POPC           451
>> CHOL             0
>> W            60817
>> NA+            678
>> CL-            671[/quote]
>>
>> where I did mistake? Does genbox reorent atom order in the -cp
>> waterSOLprot.gro -cs MEMBRANEsystem.gro ? Could it be fixed?
>>
>> 2016-04-18 16:21 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
>>> 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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