[gmx-users] Doubt regarding membrane protein in POPC bilayer

Pawan Kumar pawan.chinari at gmail.com
Tue Mar 31 13:36:29 CEST 2009


Respected Sir,

Greetings from Pawan.
Thanks for all your suggestions.
Is it possible to use the lipid.itp file from Tieleman sir's website in
combination with GROMOS 96 force field without any modification ?
Is it fine if I use the Gromos/Berger force field combination for the system
I am using ?
I am sorry to ask this but can you please help me with some information how
to modify the lipid.itp file ?
I will edit vdwradii.dat file as per your suggestion.

Thanking you,

Yours sincerely,
Pawan

On Tue, Mar 31, 2009 at 4:53 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Pawan Kumar wrote:
>
>> 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.
>>
>
> No, that is incorrect.  You need to add the additional atom type as well as
> convert C6/C12 to sigma/epsilon.  Otherwise, the calculated nonbonded
> interactions are meaningless.  Read instructions carefully!
>
> Force fields have to be internally self-consistent, so using the parameters
> from OPLS with Berger lipids will give spurious results.  The only proper
> combinations are Gromos/Berger or OPLS/converted Berger.
>
>  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.
>>
>
> No, your system will probably explode due to unsatisfied charge
> interactions and hydrogen bonds.  There is a substantial dipole in each
> lipid headgroup that can repel the lipids away from each other if it is not
> shielded.
>
>  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
>>
>
> Using a 0.5-nm radius for carbon will cause problems of excess memory
> consumption, or otherwise breaks the calculation.  Use something more along
> the lines of 0.35 or 0.375, and manually delete out any stray waters in the
> hydrophobic core.
>
> -Justin
>
>>
>> Thanking you,
>>
>> Yours sincerely,
>> Pawan
>>
>> On Tue, Mar 31, 2009 at 4:20 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> 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>
>>            <mailto: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> <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 <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
>
> ========================================
>
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