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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> > > AMBER.ambermd.org <javascript:;>
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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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> > AMBER.ambermd.org <javascript:;>
> > 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 Mon Dec 22 2014 - 19:00:02 PST
