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 - 13:30:02 PST
