[gmx-users] Doubt regarding membrane protein in POPC bilayer
Pawan Kumar
pawan.chinari at gmail.com
Tue Mar 31 13:15:38 CEST 2009
Respected Sir,
Greetings from Pawan.
I have edited the lipid.itp file to add just one line extra " H atom from
the opls_force_filed.itp " at the end of lipid interactions data and that
works fine.
I have done this after seeing the archives. It was given either I should
change the file for sigma and epsilon values or else just add this line.
I think I have done it correctly. If not please correct me.
I have removed the position restraints after the inflategro procedure.
After that I did energy minimization using define = -DFLEXIBLE.
I will change the temperature as per your suggestion.
I thought before solvating if I do position restraint mdrun the lipids will
compact more surrounding the protein.
Thats the step when I got Lincs warnings and segmentation fault.
Then I tried solvating the system using genbox step and spc216.gro as the
solvent.
But before doing the solvation step I copied the vdwradii.dat file into the
working directory and increased the value for carbon to 0.5.
But the result of this was " Segmentation fault " again. Can you please tell
me why I get the " Segmentation fault " here in this step.
The command used was : genbox -cp comp_em27.pdb -cs spc216.gro -o box.pdb
-p topol.top
Thanking you,
Yours sincerely,
Pawan
On Tue, Mar 31, 2009 at 4:20 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Justin A. Lemkul wrote:
>
>>
>>
>> Pawan Kumar wrote:
>>
>>> Respected Sir,
>>>
>>> Greetings from Pawan.
>>> I have used force constants of 100000 in position restraint .itp files
>>> for proteins as suggested in Dr. Tieleman' s webisite for Inflategro.
>>> The mdp files are :
>>>
>>
>> The .mdp files look reasonable enough, although I don't know why you are
>> applying position restraints during EM. If it is for InflateGRO, that is
>> fine, but once the system is assembled, you should remove the position
>> restraints from the protein to minimize the system more.
>>
>> And are you sure you want 300K? DPPC will be in a gel phase at that
>> temperature. If you want a more realistic fluid-phase model, you'll have to
>> go above 315K (323K is common).
>>
>>
> One thing I just noticed. You don't have solvent in your
> position-restrained run? That could be a big problem if the lipid
> headgroups are strongly repelled from one another. Add solvent before doing
> anything other than EM.
>
> -Justin
>
>
> *Topology file :*
>>> ; Include forcefield parameters
>>> #include "ffoplsaa.itp"
>>> #include "lipid.itp"
>>> #include "dppc.itp"
>>>
>>>
>> This section should not work, as written. Have you modified lipid.itp
>> according to Chris Neale's half-epsilon double-pairlist method? If not,
>> what you've done makes no sense. The Berger lipid parameters distributed
>> through Tieleman's site are designed for use with the Gromos force fields.
>> They can be modified (search in the archives), but that can also be a
>> source of error. Users who have made mistakes in the conversion have seen
>> their systems explode.
>>
>> -Justin
>>
>> ; Include chain topologies
>>> #include "topol_A.itp"
>>> #include "topol_B.itp"
>>> #include "topol_C.itp"
>>>
>>> ;#ifdef POSRES
>>> ;#include "lipid_posre.itp"
>>> ;#endif
>>>
>>> ; Include water topology
>>> #ifdef FLEX_SPC
>>> #include "flexspc.itp"
>>> #else
>>> #include "spc.itp"
>>> #endif
>>>
>>> #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
>>> PROTEIN IN DPPC BILAYER
>>>
>>> [ molecules ]
>>> ; Compound #mols
>>> Protein_A 1
>>> Protein_B 1
>>> Protein_C 1
>>> DPPC 926
>>> ;SOL 23552
>>>
>>> Please help with some suggestions.
>>>
>>> Thanking you,
>>>
>>> Yours sincerely,
>>> Pawan
>>>
>>> On Mon, Mar 30, 2009 at 6:22 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>>> jalemkul at vt.edu>> wrote:
>>>
>>> Pawan Kumar wrote:
>>>
>>> Respected Sir,
>>>
>>> Greetings from Pawan.
>>> I did the Inflategro procedure for the POPC bilayer generated
>>> using genconf.
>>> It took around 26 compressions for coming near the initial area
>>> (just above it).
>>> The minimization were all converged to Fmax < 1350.
>>> If I decrease the Fmax less than this I am getting machine
>>> precision.
>>> But when I proceeded with the final compressed structure for pr
>>> mdrun it gave lincs warnings and ended with segmentation fault.
>>> As an alternative to this bilayer I used the DPPC bilayer
>>> (pre-equilibrated) which is given in GMX-Benchmark distribution.
>>> I carried out the same steps of Inflategro. I used the cutoff of
>>> 14 A in the inflation and compression step also.
>>> In this case the the Steepest Descents converged to Fmax < 1000
>>> in all the steps. The maximum force war never above 850.
>>> But when I did position restraint mdrun with the last compressed
>>> file I got Lincs warnings and Segementation fault after few
>>> steps (30 - 40 steps).
>>> Can you please help how to proceed ?
>>>
>>>
>>> If the minimization procedure is adequately finishing, then the
>>> problem comes from something you are doing. If you post your .mdp
>>> file, we may be able to see if there are any obvious mistakes.
>>>
>>> -Justin
>>>
>>> Thanking you,
>>>
>>> Yours sincerely,
>>> Pawan
>>>
>>>
>>> Justin A. Lemkul
>>> Graduate Research Assistant
>>> ICTAS Doctoral Scholar
>>> Department of Biochemistry
>>> Virginia Tech
>>> Blacksburg, VA
>>> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>
>>> ========================================
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>>>
>>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
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> Please search the archive at http://www.gromacs.org/search before posting!
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