Thank you Dan,
I used the same script changing the last line to multihist
runanalysis multihist PROJECT:1 PROJECT:2 free 300 out fhist-all.CA.agr bins 400
The result is the same. No errors thrown out. The following files were generated. avg.nc; covmat-ca.dat; evecs-ca.dat. No histogram was produced. Here’s part of the output
[average avg.nc]
AVERAGE: Averaging over coordinates in mask [*]
Start: 1 Stop: Final frame
Writing averaged coords to [avg.nc]
[createcrd CRD1]
CREATECRD: Saving coordinates from Top 3n7h_de3_solv.prmtop to "CRD1"
[run]
MATRIX: Calculating covar matrix, output is by atom
Printing to file covmat-ca.dat
Storing matrix on internal stack with name: matrixdat
Start: 1 Stop: Final frame
Mask1: .CA
covmat-ca.dat: Writing 2D data.
[runanalysis diagmatrix matrixdat out evecs-ca.dat vecs 10 name MyEvecs]
ANALYZE MATRIX: Analyzing matrix matrixdat and dumping results to evecs-ca.dat
Calculating 10 eigenvectors
Storing modes with name: MyEvec
RMSD_00000 "RMSD_00000" (double), size is 2000
CRD1 "CRD1" (coords), size is 2000 3n7h_de3_solv.prmtop, 13273 atoms, 3882 res, box: Trunc. Oct., 3758 mol, 3747 solvent
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]
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)
> _______________________________________________
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Received on Mon Aug 03 2015 - 07:00:02 PDT
