Hi
Thanks a lot for your comment it is much appreciated.
This seems to drifting best describe what the I want to achieve and
measuring distance would be most useful I believe.
On 2 June 2014 13:59, Soumendranath Bhakat <bhakatsoumendranath.gmail.com>
wrote:
> 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
> _______________________________________________
> 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
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Received on Mon Jun 02 2014 - 05:30:05 PDT
