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
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> 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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Received on Mon Aug 03 2015 - 06:30:03 PDT
