[gmx-users] MARTINI simulation of protein-protein recognition
James Starlight
jmsstarlight at gmail.com
Tue Apr 19 16:15:02 CEST 2016
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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