Re: Simulation of a protein and calcium ions

From: Ajasja Ljubetič (
Date: Tue Oct 08 2013 - 03:29:28 CDT


Perhaps you have not been running your simulations long enough and have not
sampled the binding of ions. Perhaps you could place the ions in the
binding site and then see if/when they dissociate.

Not my field, but I have a feeling that ions are difficult to parametrize
using classical MD forcefields. Which ions are you observing (small like Na
or large like Cs?). Which forcefield? Does the forcefield have any NBFIX
parameters? Also, are the literature sources you mention based on
experimental data or simulations?

Best regards,

On 8 October 2013 10:15, Stephan Matthias Grein <> wrote:

> Hash: SHA1
> 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,
> Stephan
> - --
> M. Sc. Stephan Grein
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