Simulation of a protein and ions

From: Stephan Matthias Grein (
Date: Tue Oct 08 2013 - 03:29:05 CDT

Dear NAMD users,

after a couple of weeks learning the NAMD/VMD basics, i came up with
one question i could not figure myself:

I have generated PSF/PDB files for my protein of interest, using
consistent topoplogy and force field parameter files and a consistent
NAMD script setup. Solvated this in a waterbox with PBC according to
the manual - which works fine.

I'm now interested in observing ions moving into binding pockets of
the protein (which are reported by literature to be between some EC
domains of the protein)... for that i solvated my protein with various
concentrations using the AutoSolvation tool in VMD.

However, at neither a low nor an extraordinary (unphysiologically)
high ion concentration, i could observe ions moving into the binding
pockets of the protein and which should stay there, according to
literature, at least if the ion concentration is very high.

Is there a general failure with my procedure? If yes, would you mind
to point it out?

Thanks in advance,

M. Sc. Stephan Grein

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