'cluster' will output coordinates exactly how it received them. If
they were autoimaged prior to being clustered, they will remain that
way on output.
-Dan
On Sun, Jan 8, 2017 at 11:55 PM, Mary Varughese <maryvj1985.gmail.com> wrote:
> 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
>>
>
> _______________________________________________
> 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
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Received on Mon Jan 09 2017 - 06:30:03 PST
