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
>
>
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--
Regards/Groete/Mit freundlichen Grüßen/recuerdos/meilleures salutations/
distinti saluti/siong/duì yú/привет
Jurgens de Bruin
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Received on Mon Jun 02 2014 - 05:00:02 PDT
