[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 17:11:22 CEST 2016
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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