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> 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> 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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> > AMBER.ambermd.org
> > 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Dec 22 2014 - 17:00:02 PST
