Dan,
You mentioned that I could ask for help with clustering using ptraj... so
I'm going to ask for a little bit of help/guidance/insight.
I read through the manual, your paper, compiled ptraj, and successfully run
some test clustering.
My questions stem from the application of your paper and the implementation
of it in ptraj. Specifically, I want to make sure I'm not being overly
redundant. (I fully understand that this is more of an Art form that a
prescriptive procedure)
Not knowing what the cluster count is, it seems that the best way to
proceed is to:
1. run CobWeb (clusters -1) to get an idea of the number (range of
numbers) for natural clusters in a given data set (where the atom masks are
the same)
2. Then run averagelinkage, means, and/or SOM algorithms with cluster
values around that implicated by CobWeb and use the pSF and DBI to assess
efficacy and choose a specific cluster count. Then proceed with analysis...
I did notice that in the implementation of the agglomerative algorithms
the ClusterMerging.txt
file gives pSF and DBI values for different numbers of clusters. It was
noted that one can set clusters to 1 and then use ReadMerge to generate
other numbers of clusters. I'm not sure exactly how to use this type of
functionality, but I was wondering, can you just run cluster 1, then use
the results generated in ClusterMerging.txt to decide on the number of
clusters and critical distance (as per your paper - low DBI and high pSF)
for an agglomerative algorithm?
If I am looking to test out and compare different clustering algorithms, is
there a way to tell ptraj to NOT print out the full clusters? (if all I am
trying to do is assess the representative structures and the clustering
metrics)
Any insight would be appreciated.
Thanks,
Jonathan
On Mon, Dec 22, 2014 at 9:59 PM, Jonathan Gough <jonathan.d.gough.gmail.com>
wrote:
> As Always, Very Helpful. Thanks Dan!
>
> On Mon, Dec 22, 2014 at 9:30 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
>
>> Hi,
>>
>> The ptraj code is still there in Amber 14, it's just not built by default.
>> You need to go to the AmberTools/src/ptraj subdirectory and type 'make
>> install' (after configuring serial of course). Let me know if you hit any
>> roadblocks.
>>
>> Hope this helps,
>>
>> -Dan
>>
>> On Monday, December 22, 2014, Jonathan Gough <jonathan.d.gough.gmail.com>
>> wrote:
>>
>> > That makes sense.
>> >
>> > Have all the algorithms from your "J. Chem. Theory Comput., Vol. 3, No.
>> 6,
>> > 2007" paper been ported over to cpptraj?
>> >
>> > I just realized that ptraj is not in Amber14, do you have a
>> recommendation
>> > on how best to install/compile ptraj (AmberTools13) alongside of a
>> > pre-existing Amber14 installation?
>> >
>> > Thanks,
>> > Jonathan
>> >
>> > On Fri, Dec 19, 2014 at 11:52 AM, Daniel Roe <daniel.r.roe.gmail.com
>> > <javascript:;>> wrote:
>> >
>> > > Hi,
>> > >
>> > > The pseudo-F calculation is not yet in the released version of
>> > > cpptraj, but it has been in the development version for some time. It
>> > > might possibly be released as part of an update. You could *maybe*
>> > > calculate it manually but it would take quite a bit of scripting. You
>> > > would need to manually calculate the centroid for each cluster and a
>> > > centroid for all clusters (doing rms-fitting as necessary if that is
>> > > your distance metric), then calculate the between-group and
>> > > within-group sum of squares for each cluster. If for some reason you
>> > > really need the pseudo-F statistic right away you'll have to use
>> > > clustering in ptraj for now.
>> > >
>> > > -Dan
>> > >
>> > > On Thu, Dec 18, 2014 at 3:54 PM, Jonathan Gough
>> > > <jonathan.d.gough.gmail.com <javascript:;>> wrote:
>> > > > Dear All,
>> > > >
>> > > > Is there a way to compute the pseudo F-statistic
>> > > > (pSF), as per J. Chem. Theory Comput., Vol. 3, No. 6, 2007,
>> > > > when clustering in cpptraj?
>> > > >
>> > > > Thanks
>> > > > Jonathan
>> > > > _______________________________________________
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>> > >
>> > >
>> > >
>> > > --
>> > > -------------------------
>> > > Daniel R. Roe, PhD
>> > > Department of Medicinal Chemistry
>> > > University of Utah
>> > > 30 South 2000 East, Room 307
>> > > Salt Lake City, UT 84112-5820
>> > > http://home.chpc.utah.edu/~cheatham/
>> > > (801) 587-9652
>> > > (801) 585-6208 (Fax)
>> > >
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>> > >
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>>
>>
>> --
>> -------------------------
>> Daniel R. Roe, PhD
>> Department of Medicinal Chemistry
>> University of Utah
>> 30 South 2000 East, Room 307
>> Salt Lake City, UT 84112-5820
>> http://home.chpc.utah.edu/~cheatham/
>> (801) 587-9652
>> (801) 585-6208 (Fax)
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Sun Jan 04 2015 - 10:30:02 PST
