From: Stephan Matthias Grein (grein_at_informatik.uni-frankfurt.de)
Date: Tue Oct 08 2013 - 04:49:53 CDT
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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