>
>
> RMSD_00002 "RMSD_00002" (double), size is 2000
> matrixdat "matrixdat" (matrix), size is 70875
> MyEvecs "MyEvecs" (modes), size is 10
> [crdaction CRD1 projection PROJECT modes MyEvecs beg 1 end 2 @CA]
>
I really need to see the entire output. If this is where your calculation
stops then clearly something is wrong because the histogram command isn't
even attempted. Are you certain you don't get any 'Warning:' or 'Error:'
messages? Also what version of cpptraj is this? (cpptraj --version)
-Dan
>
>
> Running hist and generating a gnu output file also fails to generate a
> histogram
>
> runanalysis hist PROJECT:1 PROJECT:2 free 300 out fhist-all.CA.gnu bins
> 400
>
> has the same effect. Same files generated but no histogram
>
> Regards
>
> George
>
>
> > On 3 Aug 2015, at 16:14, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >
> > Hi,
> >
> > Were there any Warning or Error messages printed by cpptraj? I think the
> > problem here is you are creating a 2D histogram with 'hist' but writing
> to
> > a format that doesn't support 2D writes (agr). Try a different output
> > format (like gnu) or use 'multihist' to create two 1D histograms.
> >
> > -Dan
> >
> > On Mon, Aug 3, 2015 at 4:46 AM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> I’m trying to conduct a PCA analysis of a trajectory, based on earlier
> >> suggestions from the amber list (10 March 2015).
> >>
> >> Below is the script that I used. It seems to run as expected or almost
> as
> >> expected because it fails to generate the histogram as given in the last
> >> line of the input script.
> >>
> >> I’d be grateful for any suggestions dealing with this problem.
> >>
> >> Regards
> >>
> >> George
> >>
> >>
> >> parm 3n7h_de3_solv.prmtop
> >> trajin prod_0-20ns.nc
> >> rms first
> >> average avg.nc
> >> createcrd CRD1
> >> run
> >> reference avg.nc [ref1]
> >> crdaction CRD1 rms .CA ref [ref1]
> >> crdaction CRD1 matrix covar name matrixdat @CA out covmat-ca.dat
> >> runanalysis diagmatrix matrixdat out evecs-ca.dat vecs 10 name MyEvecs
> >> run
> >> crdaction CRD1 projection PROJECT modes MyEvecs beg 1 end 2 @CA
> >> runanalysis hist PROJECT:1 PROJECT:2 free 300 out fhist-all.CA.agr bins
> >> 400
> >> _______________________________________________
> >> AMBER mailing list
> >> 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)
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> 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)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 03 2015 - 07:30:02 PDT
