Sir,
I am trying to do a second clustering on the output of a first
clustering ie on the most populated cluster.
As you suggested i do strip and autoimage my trajectory before
clustering ( a receptor- ligand system).
My doubt is that whether the clustered trajectories that i get with
the command option "clusterout cluster clusterfmt amber" would also be
under autoimage.? i want to do a clustering on the most populated
cluster. and i also want to do mmpbsa on it.
Thanking you
mary
On 1/9/17, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Autoimaging prior to clustering is only necessary if your distance
> metric will involve more than 1 molecule, e.g. the conformation of a
> protein dimer. Otherwise it doesn't matter.
>
> -Dan
>
> On Sat, Jan 7, 2017 at 5:33 AM, Mary Varughese <maryvj1985.gmail.com>
> wrote:
>> Sir
>>
>> before i perform cluster on my trajectory i had done autoimage.
>> since i had included the option for cluster trajectories, trajectory
>> corresponding to each cluster was also formed.
>> I tried to cluster the most populated cluster again. i want to know
>> whether the cluster trajectories formed in the first step is
>> autoimaged? or should i autoimage that again before i do my second
>> cluster?
>>
>>
>>
>>
>> On 1/5/17, Mary Varughese <maryvj1985.gmail.com> wrote:
>>> Thank you very much.
>>>
>>> It was very much helpful especially that script in supp material.
>>>
>>> Thank you
>>>
>>> On Thu, Jan 5, 2017 at 7:00 PM, Daniel Roe <daniel.r.roe.gmail.com>
>>> wrote:
>>>
>>>> See also the clustering script in part 7 of the supporting info here:
>>>> http://pubs.acs.org/doi/abs/10.1021/jp4125099
>>>>
>>>> -Dan
>>>>
>>>> On Thu, Jan 5, 2017 at 7:48 AM, Christina Bergonzo
>>>> <cbergonzo.gmail.com>
>>>> wrote:
>>>> > Hi,
>>>> >
>>>> > You can take a look at the supporting information of this paper:
>>>> > Highly sampled tetranucleotide and tetraloop motifs enable evaluation
>>>> > of
>>>> > common RNA force fields
>>>> > <https://scholar.google.com/citations?view_op=view_citation&hl=en&user=
>>>> d4JoelsAAAAJ&citation_for_view=d4JoelsAAAAJ:In6cVmBjs0IC>
>>>> > C Bergonzo, NM Henriksen, DR Roe, TE Cheatham
>>>> > RNA 21 (9), 1578-1590
>>>> >
>>>> > http://rnajournal.cshlp.org/content/suppl/2015/06/19/rna.
>>>> 051102.115.DC1/SuppMaterial.pdf
>>>> >
>>>> > There is a CPPTRAJ command which performs combined clustering on 8
>>>> > trajectories.
>>>> >
>>>> > Hope this helps,
>>>> > Christina
>>>> >
>>>> > On Thu, Jan 5, 2017 at 5:59 AM, Mary Varughese <maryvj1985.gmail.com>
>>>> wrote:
>>>> >
>>>> >> Sir
>>>> >>
>>>> >>
>>>> >> in combined clustering, could i compare more than two trajectories?
>>>> >> If
>>>> >> so is there any difference in the command option
>>>> >> split ..Frameno...
>>>> >>
>>>> >> Also in split_summary.dat is there any useful information.
>>>> >>
>>>> >> how could i infer the convergence of the trajectory DBI , pSF
>>>> >>
>>>> >> Please give me some idea
>>>> >>
>>>> >>
>>>> >> Thanking you
>>>> >>
>>>> >>
>>>> >> mary varughese
>>>> >>
>>>> >> _______________________________________________
>>>> >> AMBER mailing list
>>>> >> AMBER.ambermd.org
>>>> >> http://lists.ambermd.org/mailman/listinfo/amber
>>>> >>
>>>> >
>>>> >
>>>> >
>>>> > --
>>>> > ------------------------------------------------------------
>>>> ---------------------------
>>>> > Christina Bergonzo
>>>> > Postdoctoral Researcher
>>>> > Department of Medicinal Chemistry, University of Utah
>>>> > http://home.chpc.utah.edu/~cheatham/
>>>> > ------------------------------------------------------------
>>>> ---------------------------
>>>> > _______________________________________________
>>>> > AMBER mailing list
>>>> > AMBER.ambermd.org
>>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>>
>>>> --
>>>> -------------------------
>>>> Daniel R. Roe
>>>> Laboratory of Computational Biology
>>>> National Institutes of Health, NHLBI
>>>> 5635 Fishers Ln, Rm T900
>>>> Rockville MD, 20852
>>>> https://www.lobos.nih.gov/lcb
>>>>
>>>> _______________________________________________
>>>> 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
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sun Jan 08 2017 - 21:00:02 PST
