[gmx-users] Abnormal popc struture after inserting protein

minnale minnale_gnos at rediffmail.com
Wed Jul 2 12:46:07 CEST 2008


  

Thanks alot Justin
I will do it in the way you suggested.

On Wed, 02 Jul 2008 Justin A.Lemkul wrote :
>
>
>minnale wrote:
>>
>>  
>>
>>Thanks to Justin for comment about my problem
>>I will tell you clearly
>>1. Initially POPC bilayer taken from Tieleman website and run the simulation for 5ns.
>>2. Protein also has taken and simulated for 9ns actually this contain 10 helices among that 10 helices two helices have taken, because i want only 2 and generated .top file for 2 helices by using *pdb2gmx command.
>>3. By using VMD orient 2 helices properly in POPC bilayer
>>4. BY using genbox command these helices embedded into POPC
>>5. Minimisation has done, it ran fine without error but it didnt reach FMAX<1000
>>6. Ran restarin with fc1000 showed the abnrmal POPC and water molecules stucture.
>>  
>
>All of that seems reasonable enough.  There are two possibilities that come to mind for things that might be of issue:
>
>1. Run the simulation longer (see my previous message).
>2. I have previously helped another user determine that their system was of insufficient size, i.e. the water layer above and below the bilayer was too small, and they were seeing artefacts of periodic boundaries (the lipid headgroups were "seeing" each other and were distorting accordingly.
>
>Assure that your system is of adequate dimensions to eliminate possibility #2, and otherwise just run a few ns of MD and see if the lipids equilibrate.
>
>-Justin
>
>>   Earlier I have run similar system with ffgmx FF with similar time 50 ps restrain that structure pretty fine.The idea of simulating system with short time is if it runs fine with short time I will give long step.
>>
>>Toplogy file is
>>
>>; Include forcefield parameters
>>#include "ffoplsaa.itp"
>>#include "popc.itp"
>>
>>[ moleculetype ]
>>; Name            nrexcl
>>Protein            3
>>
>>[ atoms ]
>>;  nr      type  resnr residue  atom  cgnr    charge      mass  typeB    chargeB      massB
>>     1  opls_287      1    ALA      N      1      -0.3    14.0067  ; qtot -0.3
>>     2  opls_290      1    ALA    H1      1      0.33      1.008  ; qtot 0.03
>>     3  opls_290      1    ALA    H2      1      0.33      1.008  ; qtot 0.36
>>     4  opls_290      1    ALA    H3      1      0.33      1.008  ; qtot 0.69
>>     5  opls_293B      1    ALA    CA      1      0.25    12.011  ; qtot 0.94
>>     6  opls_140      1    ALA    HA      1      0.06      1.008  ; qtot 1
>>     7  opls_135      1    ALA    CB      2      -0.18    12.011  ; qtot 0.82
>>     8  opls_140      1    ALA    HB1      2      0.06      1.008  ; qtot 0.88
>>     9  opls_140      1    ALA    HB2      2      0.06      1.008  ; qtot 0.94
>>     10  opls_140      1    ALA    HB3      2      0.06      1.008  ; qtot 1
>>     11  opls_235      1    ALA      C      3        0.5    12.011  ; qtot 1.5
>>     12  opls_236      1    ALA      O      3      -0.5    15.9994  ; qtot 1
>>     13  opls_238      2    VAL      N      4      -0.5    14.0067  ; qtot 0.5
>>     14  opls_241      2    VAL      H      4        0.3      1.008  ; qtot 0.8
>>     15  opls_224B      2    VAL    CA      4      0.14    12.011  ; qtot 0.94
>>     16  opls_140      2    VAL    HA      4      0.06      1.008  ; qtot 1
>>   .
>>   .
>>   .
>>   .
>>   .
>>   .
>>   .
>>   .
>>   .
>>   .
>>; Include Position restrain protein
>>#ifdef POSRES_PROTEIN
>>#include "posre.itp"
>>#endif
>>
>>;Include Position restrain lipid
>>#ifdef POSRES_LIPID
>>#include "lip_posre.itp"
>>#endif
>>
>>; Include water topology
>>#include "spc.itp"
>>
>>#ifdef POSRES_WATER
>>; Position restraint for each water oxygen
>>[ position_restraints ]
>>;  i funct      fcx        fcy        fcz
>>   1    1      1000      1000      1000
>>#endif
>>
>>; Include generic topology for ions
>>#include "ions.itp"
>>
>>[ system ]
>>; Name
>>GROtesk MACabre and Sinister in water
>>
>>[ molecules ]
>>; Compound        #mols
>>Protein            1
>>POPC              94
>>SOL              2434
>>CL-                3
>>
>>Any comments wiill be appreciated.
>>
>>Thanks in advance
>>
>>  
>>
>>
>>
>>On Tue, 01 Jul 2008 Justin A.Lemkul wrote :
>> >
>> >
>> >minnale wrote:
>> >>
>> >>
>> >>  So I dont boughter about those sentences because I confirmed in list archives that I can proceed further steps and moreover em.gro file is      fine, so I went for restrain, here I am getting abnormal POPC structure
>> >>means POPC tails are tilting, water molecules structure also disturbed.
>> >>
>> >>Could you please tell me where iam doing mistake?
>> >>
>> >
>> >Not really.  You haven't told us much.  What parameters are you using (for the protein and the lipids)?  How did you insert your protein?
>> >
>> >Also realize that 50 ps is *extremely* short in the realm of membrane protein MD.  Even after several hundred picoseconds things may look a bit strange.  Prevailing wisdom is that between 25-30 ns of MD are required for the lipids to reach equilibrium (although they should look reasonable after just a few ns, but parameters like area per headgroup may not level off for a while).
>> >
>> >-Justin
>> >
>> >>my pr.mdp filetitle              =  protein in popc restrained
>> >>define              =  -DPOSRES_protein
>> >>constraints        =  all-bonds
>> >>integrator          =  md
>> >>dt                  =  0.002    ; ps !
>> >>nsteps              =  10000    ; total 50 ps.
>> >>nstcomm            =  1
>> >>nstxout            =  50
>> >>nstvout            =  1000
>> >>nstfout            =  0
>> >>nstlog              =  10
>> >>nstenergy          =  10
>> >>nstlist            =  10
>> >>ns_type            =  grid
>> >>rlist              =  0.9
>> >>coulombtype        =  PME
>> >>rcoulomb            =  0.9
>> >>rvdw                =  1.4
>> >>pbc                =  xyz
>> >>; Berendsen temperature coupling is on in three groups
>> >>Tcoupl              =  Berendsen
>> >>tc-grps            =  POPC    Protein  SOL_CL-
>> >>tau_t              =  0.1      0.1      0.1
>> >>ref_t              =  310      310      310
>> >>; Anisotropic pressure coupling is now on
>> >>Pcoupl              =  berendsen
>> >>pcoupltype          =  anisotropic
>> >>tau_p              =  1.0      1.0    1.0    0        0      0
>> >>compressibility    =  4.5e-5  4.5e-5  4.5e-5  0        0      0
>> >>ref_p              =  1.0      1.0    1.0    0        0      0
>> >>; Energy monitoring
>> >>energygrps          =  POPC  Protein  SOL_CL-
>> >>; Generate velocites is on at 300 K.
>> >>gen_vel            =  yes
>> >>gen_temp            =  310.0
>> >>gen_seed            =  173529
>> >>
>> >>Thanks in advance.                     >>
>> >>
>> >>------------------------------------------------------------------------
>> >>
>> >>_______________________________________________
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>> >
>> >-- ========================================
>> >
>> >Justin A. Lemkul
>> >Graduate Research Assistant
>> >Department of Biochemistry
>> >Virginia Tech
>> >Blacksburg, VA
>> >jalemkul[at]vt.edu | (540) 231-9080
>> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>> >
>> >========================================
>> >
>>
>>
>>
>>------------------------------------------------------------------------
>>
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>>gmx-users mailing list    gmx-users at gromacs.org
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>
>-- ========================================
>
>Justin A. Lemkul
>Graduate Research Assistant
>Department of Biochemistry
>Virginia Tech
>Blacksburg, VA
>jalemkul[at]vt.edu | (540) 231-9080
>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
>========================================
>
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