Hi,
On Thu, Jan 8, 2015 at 9:20 AM, Jonathan Gough
<jonathan.d.gough.gmail.com> wrote:
> Can ptraj write trajectories as netcdf? what is the most compact way of
> writing trajectories as the output of a clustering in ptraj
>
> when I tried using 'netcdf' or 'cdf' for all, I got "WARNING: invalid file
> format netcdf/cdf!"
>
> am I missing something?
No, unfortunately I don't think netcdf writes were enabled for
clustering output in ptraj. That is a cpptraj-only feature.
-Dan
>
> On Sun, Jan 4, 2015 at 1:05 PM, Jonathan Gough <jonathan.d.gough.gmail.com>
> wrote:
>
>> 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
>>>> > > > _______________________________________________
>>>> > > > AMBER mailing list
>>>> > > > AMBER.ambermd.org <javascript:;>
>>>> > > > http://lists.ambermd.org/mailman/listinfo/amber
>>>> > >
>>>> > >
>>>> > >
>>>> > > --
>>>> > > -------------------------
>>>> > > 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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--
-------------------------
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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Received on Thu Jan 08 2015 - 09:00:05 PST
