The drifting phenomena you can easily check by taking snapshots. Use
CPPTRAJ for that. "movement" can be measured in different chemical physics
terms such as distance, Rg, but you want to see drifting of ligand across
two different active sites so you focus on snapshots and measure distance
between certain parameters which you defined it is upto you.
All the best!!
On Mon, Jun 2, 2014 at 1:31 PM, Jurgens de Bruin <debruinjj.gmail.com>
wrote:
> Hi,
> Thanks for the reply. I apologies for not being clear by using the term
> "movement". I hope this makes it more clear, I have done a docking study
> using Dock6 the results show 2 possible docking sites that are adjacent to
> each-other, I was hoping to show using MD that the ligand would be able to
> move from one docking site to the next.
>
>
>
>
> On 2 June 2014 13:25, Jason Swails <jason.swails.gmail.com> wrote:
>
> > On Mon, 2014-06-02 at 04:20 +0200, Jurgens de Bruin wrote:
> > > Hi All,
> > >
> > >
> > > Firstly I am new to AMBER and MD of proteins. I have been working on
> > > Homology Modeling and Docking for 2years now and would like to start
> > using
> > > AMBER for MD purposes.
> > >
> > > I do hope someone can be of assistance, I would like to know if it
> would
> > be
> > > possible to track the movement of a ligand within a protein cavity
> using
> > > AMBER and if so point me in the correct direction?
> >
> > You have to apply a geometric definition of what you mean by "movement".
> > For example, certain distances or angles between atoms or centers of
> > mass of different atom groups. Or a root mean squared deviation of the
> > ligand atoms following a RMSD-based fit of the protein.
> >
> > All of this trajectory analysis can be run with the "cpptraj" program of
> > AmberTools, but you must first devise a rigorous definition of what you
> > want to quantify (or qualify).
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
> distinti saluti/siong/duì yú/привет
>
> Jurgens de Bruin
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Mon Jun 02 2014 - 05:30:02 PDT
