Re: Simulation of a protein and calcium ions

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Oct 08 2013 - 08:21:38 CDT

Have not used autionze for some time. But are you sure you're not losing
the calcium at psfgen stage?
You can also manually add ions manually and solvate or try the charmm-gui
solvator http://www.charmm-gui.org/?doc=input/solvator.

Regards,
Ajasja

On 8 October 2013 11:49, Stephan Matthias Grein <
grein_at_informatik.uni-frankfurt.de> wrote:

> Thank you.
>
> I see another problem, if i use AutoIonize Plugin, then my Calcium ions
> get removed in my (ionized.psf and ionized.pdb) file -> is this the case
> which i should expect?
>
> All the best,
> Stephan
> Am 10/8/13 11:08 AM, schrieb Ajasja Ljubetič:
> > 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
> > crystalogrphically resovled.
> >
> > Regards,
> > Ajasja
> >
> >
> > On 8 October 2013 10:43, Stephan Matthias Grein <
> > grein_at_informatik.uni-frankfurt.de> wrote:
> >
> > 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,
> > Stephan
> >
> > 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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