From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Oct 08 2013 - 03:29:40 CDT
On Tue, Oct 8, 2013 at 10:15 AM, Stephan Matthias Grein
<grein_at_informatik.uni-frankfurt.de> wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> 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?
have you considered the time scale on which an ion would move in a
binding pocket?
have you considered that there is a energetic component (you may have
to cross energy barriers), but also a statistical component (the ion
has to "find" the path towards the binding site)?
axel.
>
> Thanks in advance,
> Stephan
>
> - --
> M. Sc. Stephan Grein
> -----BEGIN PGP SIGNATURE-----
> Version: GnuPG v1.4.14 (Darwin)
> Comment: Using GnuPG with Thunderbird - http://www.enigmail.net/
>
> iQIcBAEBAgAGBQJSU78vAAoJEH3H1/1zsiJL/+4P/0sOpxSC5VXA5Wkb9HIsnqnx
> eLS6VC1qe9NVao+t+MicNne2+KFOLXPcRnGwzEHowsZUHdAsJtYmL7MqyhGOOw2i
> v5v5bElaoU39jwycgtJxfFvac8e3Gl0977vMAIazdwFeme0+uWUSZ7hKVLtCs3mL
> SokeZZNK2VVmlvcR9oLO5c7tKQwDMP9SXZaHLWV3FsvU4Ym170jdQLOok4gydFTg
> NpdY20Lei2v5jZEohcPiWVlOHBKlu4hJUqRNXjkcNH5q9dMINunCwqnCQKTnKM7m
> 63WqOQPE/e6N7t02T5fpwDV/42iLxqvaIaNxg67vVr0DuKS7MlebR+sd+3L8ZvfQ
> 5dCW7NPvMfPEdzc724NYHw1+BKCIPqqb+/5uoMa7O/+cB2N4YmxrjGJhGR7Z2WiO
> b8KFrLoR6Jr5QRWjPtE5NDAVwAZdIOI/ywsu50HsX+ByzENnSNCz4bmUPcfh2lnr
> XNLUjdiLhSmWL2/gWhxC+9batBBMeYRz6n84BB4TqQCud3U3dyoLFIAP6ij6Bt1Z
> PyvHTOMOksfKWrwxzMv4RybzbF/QJVqvxveQ8GpcaD6c/O/o0fXwIkXxv2GY4bmx
> uWxqW8fwsQTCPiyPJ0W7sLIgGBXZ8HXGmT1yHgMKSFhlfyPNeqBBqtrVAly3RsV/
> yX7bhyURpqFrF2uOI3Yk
> =K6jY
> -----END PGP SIGNATURE-----
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 International Centre for Theoretical Physics, Trieste. Italy.
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:21:45 CST