Hi,
I am working on the Tutorial as suggested, I have a question about the
Density Graph as my graph is not reaching a plateau, should I increase the
cycles?
On 3 June 2014 08:09, Jurgens de Bruin <debruinjj.gmail.com> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>> _______________________________________________
>> 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
>
--
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
Received on Wed Jun 04 2014 - 05:30:02 PDT
