From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Oct 08 2013 - 04:08:56 CDT
It's good form to always keep the mailing list among the recipients.
Well you should read the relevant papers in detail, but from a quick glance
at http://www.ks.uiuc.edu/Research/cadherin/ it seems that they started
from Ca ions in the binding site, since the mention the ions were
On 8 October 2013 10:43, Stephan Matthias Grein <
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> Hi thanks for your answers.
> In fact I'm using Calcium ions and N-Cadherins.
> I simulated for 5 ns ... this could be probably too short, thank you!
> I will try for longer runs.
> The literature data is from simulations of C-Cadherin with Calcium,
> which were performed with NAMD.
> I have _no_ NBFIX terms for any ion.
> All the best,
> Am 10/8/13 10:29 AM, schrieb Ajasja Ljubetič:
> > Hi,
> > 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, Ajasja
> > On 8 October 2013 10:15, Stephan Matthias Grein <
> > grein_at_informatik.uni-frankfurt.de> wrote:
> > 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
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