[gmx-users] MARTINI simulation of protein-protein recognition
James Starlight
jmsstarlight at gmail.com
Wed Apr 20 11:14:12 CEST 2016
Yes actually I did this but by hands which was not very comfortable :-)
Hope that martini developers will add possibility to make such kind of
systems more trivially :-)
J.
2016-04-19 17:11 GMT+02:00 <jkrieger at mrc-lmb.cam.ac.uk>:
> ok shouldn't martinize do the equivalent to pdb2gmx, i.e. make the final
> pdb or gro file and a corresponding topology? Your problem is with genbox
> with thinks MEMBRANEsystem.gro is the solvent and therefore will not be
> connected like protein and membrane. My suggestion to take the placements
> from genbox but remake the pdb can presumably still be done to make input
> for martinize just like it could for pdb2gmx.
>
> Best wishes
> James
>
>> no pdb2gmx will not work because I am working with the martini CG models
>>
>> how I fix the issue it reorent the atom names by hands (coppy protein
>> and lipids from the initial pdbs which were submitted to genbox to the
>> complex.gro because initially I had properly oriented complexes).
>>
>> BTW where I can find smth useful regarding mdp options for the system
>> which include 2 unbound protein comlexes. E.g how it better to define
>> coupling groups for the barostat and thermostat assuming that 1
>> proteis is inserted within the membrane and another is within the
>> water.
>>
>> Thanks!!!
>>
>> J.
>>
>> 2016-04-19 15:54 GMT+02:00 <jkrieger at mrc-lmb.cam.ac.uk>:
>>> 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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