[gmx-users] Re: Doubt regarding membrane protein in POPC bilayer
Justin A. Lemkul
jalemkul at vt.edu
Tue Mar 31 14:20:37 CEST 2009
Pawan Kumar wrote:
> 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
> <http://wiki.gromacs.org/membrane-simulations> for solvation after the
> genbox step to remove extra waters from the hydrophobic part of the
> bilayer ?
>
You mean the C program or shell script at
http://wiki.gromacs.org/index.php/Membrane_Simulations? Yes, either of those
should be fine.
-Justin
> Thanking you,
>
> Yours sincerely,
> Pawan
>
> On Tue, Mar 31, 2009 at 5:31 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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>>
> <mailto: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>>>
> <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 <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> <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>
> <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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