[gmx-users] Doubt regarding membrane protein in POPC bilayer
Pawan Kumar
pawan.chinari at gmail.com
Tue Mar 31 14:17:52 CEST 2009
Respected Sir,
Greetings from Pawan.
Thanks for all your kind help and suggestions.
I will work on this and ask you if I have further doubts.
Is it fine if I use the perl code given in
wiki.gromacs.org/membrane-simulations for solvation after the genbox step to
remove extra waters from the hydrophobic part of the bilayer ?
Thanking you,
Yours sincerely,
Pawan
On Tue, Mar 31, 2009 at 5:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Pawan Kumar wrote:
>
>> 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 ?
>>
>
> If you want to use lipid.itp without any modification, you are restricted
> to the ffgmx (deprecated!) force field. For Gromos96-lipid.itp combination,
> simply remove the ";; parameters for lipid-GROMOS interactions," as these
> nonbonded combinations are for ffgmx only. Otherwise, the nonbonded
> interactions (which now have consistent combination rules) should be
> generated correctly.
>
> Is it fine if I use the Gromos/Berger force field combination for the
>> system I am using ?
>>
>
> That is a decision you will have to make based on a thorough examination of
> the literature, and the benefits and criticisms of these particular force
> field parameters.
>
> I am sorry to ask this but can you please help me with some information
>> how to modify the lipid.itp file ?
>>
>
> That depends entirely upon what you want to do. If you want Gromos/Berger,
> I've already told you. If you want OPLS/modified Berger, search the
> archives for Chris Neale's posts on that topic.
>
> -Justin
>
> 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<mailto:
>> 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>
>> <mailto: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>>
>> <mailto: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> <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> <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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> gmx-users mailing list gmx-users at gromacs.org
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