Thanks Jason,
Like the tutorial, the complex started out sans H2O, and was then solvated
(that's when the Na atom was added). I believe the mmpbsa script uses the
inpcrd files for the original complex, the ligand, and the receptor,
therefore I figured somewhere in there it get's rid of the extra water and
the sodium atom. But I wanted to double check.
I already did the simulations... not to do the binding calculation...
On Mon, Dec 3, 2012 at 4:08 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Mon, Dec 3, 2012 at 3:29 PM, Jonathan Gough
> <jonathan.d.gough.gmail.com>wrote:
>
> > I apologize in advance if this is rudimentary...
> >
> > I'm looking a protein-peptide binding interaction 87 residues - and 19
> > residues (complex 106).
> >
> > Using the well written tutorials and literature I believe i followed the
> > steps correctly. (minimization, heating, acquiring an equilibrium state)
> > Then I did the "production" run (10 - 5ns simulations, snapshots every 5
> > picoseconds) I believe that I now have 50ns of simulation with 5000
> frames.
> >
> >
> > Questions:
> > 1: - are 5000 frames too many?
> >
>
> It depends -- how long does it take to finish the calculation? If it takes
> too long, then yes, 5000 is too many :). You can test it out with GB --
> does you answer change much using 5000 instead of 500 frames? (Is it even
> statistically relevant?) (Note, use 500 interspersed snapshots, not 500
> all at the beginning).
>
> 2: - a sodium atom was added (via addionsrand) to neutralize the system.
> > Would I be correct in assuming that I don't need to worry about that?
> > (it's not in the receptor or ligand file, only the solvated file)
> >
>
> You should always try to avoid using explicit ions in implicit solvent
> calculations. Counter ion effects are taken care of within the model
> itself (it is the Boltzmann part of the Poisson-Boltzmann equation, and GB
> has a Debye screening parameter that models the electrostatic screening
> effect that ions have).
>
> Good luck,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon Dec 03 2012 - 14:00:03 PST
