Hi,
For backwards compatibility with ptraj, cpptraj forces matrix output
into a certain format. To override this you can create the file
manually, e.g.
matrix correl :1-450.CA byatom name MyMatrix
create matrix.gnu MyMatrix
I should probably revisit this behavior since it has been a while
since ptraj has been in AmberTools...
Hope this helps,
-Dan
On Tue, Apr 30, 2019 at 1:00 PM anu chandra <anu80125.gmail.com> wrote:
>
> Hello Amber users,
>
> I am trying to visualize the matrix output from cross correlation analysis
> in gnuplot, by using a .gnu extension. However, gnu output file failed have
> required gnuplot heads. The following cpptraj command was used for the
> analysis.
>
> parm parm.top
>
> trajin 1md.nc
> trip :WAT,Na+
> autoimage origin
>
> reference pdb1.pdb
> rms reference out rmsd_CA_1-450.txt :1-450.CA
>
> matrix correl :1-450.CA out matrix.gnu byatom
>
> However, the file 'matrix.gnu' do not have the required gnuplot labels.
>
> 1.000 1.000 1.000
> 1.000 2.000 0.814
> 1.000 3.000 0.568
> 1.000 4.000 0.354
> 1.000 5.000 0.182
>
> Any help would be highly appreciated
>
>
> Many thanks in advance
> Anu
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Received on Thu May 02 2019 - 06:00:02 PDT
