[gmx-users] MARTINI simulation of protein-protein recognition
James Starlight
jmsstarlight at gmail.com
Tue Apr 19 15:14:25 CEST 2016
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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