Thanks for the reply. I know that charmm-gui online server can built
membrane protein for a given composition. Can you suggest any other
reliable online tools?
mani
On Sun, Jan 20, 2013 at 8:54 PM, Aron Broom <broomsday.gmail.com> wrote:
> 1) If you don't think the protein is solvated inside the membrane (which
> seems pretty unlikely) you should remove them. For the water to leave the
> membrane through minimization or MD may take an extremely long time.
>
> 2) You should be able to estimate that distance from known crystal
> structures of membrane proteins that were solved with detergent molecules
> present. I would guess something along the order to ~2 Angstroms
>
> 3) If you do this, you'll have to re-equilibrate after.
>
> In general you should estimate the equilibration of the system in two ways:
>
> A) the RMSD of the protein (it should become constant)
>
> B) the potential energy of the system. Since you are running at constant
> temperature, the energy may change over time (it is not a constant energy
> simulation), but nevertheless you expect the potential energy to settle out
> to some extent as it reaches a more natural configuration. You could also
> consider looking at the pressure, and expect to see it equilibrate.
>
> What do you mean by "restraints" on the protein and the membrane? I don't
> see why the membrane or counterions should be restrained at all, and the
> protein should potentially only be restrained initially to a particular
> position in the membrane or to within a certain RMSD to ensure it doesn't
> unfold if the initial placement is very bad.
>
> There are tools online that allow you to for instance make a membrane
> bilayer of a particular composition and insert a protein into it. That is,
> they will automatically calculate which membrane lipids should be removed
> to fit the protein without overdoing it. This might allow for faster
> equilibration than the big cylindrical hole you are now making, but perhaps
> its not worth it.
>
> ~Aron
>
> On Sun, Jan 20, 2013 at 7:59 PM, Manikanthan Bhavaraju <
> manikanthanbhavaraju.gmail.com> wrote:
>
> > Dear All,
> >
> > I am simulating a membrane bound protein using amber12 and Lipid11 and
> > ff99SB force fields. The initial 20 residues of the protein goes into the
> > membrane layer. Therefore, I have taken a pre-equilibrated POPC
> membrane
> > layer (256 POPC molecules) which has cylindrical hole of (radius = 12
> ang)
> > in the center. I have manually inserted 1-20 residues of the protein
> > using VMD and capped rest of the protein with the solvent box.
> Similarly,
> > the cholesterol molecules were also manually added. While solvating the
> > system, VMD has added water molecules around the protein which was
> inserted
> > in the membrane. I have few questions about this system:
> >
> > 1.Do I have to remove those water molecules manually before I start the
> > simulation?
> >
> > 2. What should be minimum distance between the protein residues (inserted
> > in the membrane layer) and the POPC molecules?
> >
> > 3. Can I remove the water molecules (present between the protein and
> > membrane) after the system have attained a constant density?
> >
> > Currently, I am simulating the system with following steps:
> >
> > 1. minimizing with restraining the protein, POPC, cholesterol, and
> > counterions for 10000 steps
> > 2. minimization for 10000 steps without any restrains
> > 3. Heating (0-100K) with constraining the protein (10 kcal/mol/ang^2) and
> > lipid (5 kcal/mol/ang^2) for 20ps under NVT
> > 4. Heating (100-300K) under NPT conditions for 100ps with same restrains
> > 5. Equilibrating the system under NPT with npt =2, with similar
> restrains.
> >
> >
> > I have equilibrated the system for 5ns. I have verified temperature,
> > volume, pressure, box dimensions, and density until now
> >
> > temperature - constant at 300k
> > volume - is changing
> > box dimensions - changing
> > density - varying in between 0.98-0.87
> >
> > So, I think the system is under the process of equilibration. Any
> anybody
> > comment on my three questions?
> >
> > manikanthan
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Manikanthan Bhavaraju
Graduate Teaching Assistant
Dept. of Chemistry
Mississippi State University
office no : 662-325-4633
MS -39762
USA.
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Received on Sun Jan 20 2013 - 20:30:02 PST
