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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>
>
> --
> -------------------------
> 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 Mon Dec 22 2014 - 19:00:03 PST
