Thanks for all the suggestions, I will try this out!
On 2 June 2014 15:12, Aldo Segura <asegurac666.yahoo.com.mx> wrote:
>
> Hi,
> When you said 2 possible binding-sites, you mean 2 high ranked poses? In
> addition to the other comments, you could run two different simulations
> each one for pose (binding site). Then, you can perform a comparative
> analysis by applying the analysis suggested in the Jason and Soumendranath
> emails.
>
> Best,
>
> Aldo
>
>
> =======================================
> Aldo Segura-Cabrera
> Postdoctoral Fellow
> Division of Experimental Hematology and Cancer Biology
> Cancer and Blood Diseases Institute
> Cincinnati Children's Hospital Medical Center
> 3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
>
> =========================================
>
>
> El Lunes, 2 de junio, 2014 8:30:32, Jurgens de Bruin <debruinjj.gmail.com>
> escribió:
>
>
>
> 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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>
--
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 - 23:30:02 PDT
