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

James Starlight jmsstarlight at gmail.com
Tue Apr 19 15:40:20 CEST 2016


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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