Dear Amber experts,
I’m trying to automate the selection of the pcmin/pcmax values of the ‘modes' command, to generate pseudo-trajectories along the PC’s of motion.I know that I can set them manually by looking at the histogram (actually gaussian kde, but I guess it’s the same) of the PC projection, but I’d like cpptraj to do that job.
The file I’m loading into cpptraj looks like so:
> $ head PC1_proj.dat
> #Frame kde_00026 kde_00027 kde_00028
> -261.602 0.0001 0.0000 0.0000
> -260.419 0.0001 0.0000 0.0000
> -259.236 0.0001 0.0000 0.0000
> -258.053 0.0001 0.0000 0.0000
> -256.870 0.0002 0.0000 0.0000
> -255.686 0.0002 0.0000 0.0000
> -254.503 0.0002 0.0000 0.0000
> -253.320 0.0002 0.0000 0.0000
> -252.137 0.0002 0.0000 0.0000
I know from the manual that cpptraj has min() and max() commands that can work on a 1D dataset. I’m loading the previous data file with:
> > readdata ./PC1_proj.dat name proj
> Reading './PC1_proj.dat' as Standard Data File with name 'proj'
> DataFile ./PC1_proj.dat has 4 columns, 401 lines.
> DataFile contains labels:
> 1: Frame
> 2: kde_00026
> 3: kde_00027
> 4: kde_00028
> Index column is 1
But I’m failing to subset the 1D ‘Frame’ data, from which I want to extract the min and max values. Below are the commands that I’ve tried, with no success:
> > proj[Frame]
> Warning: Data set 'proj[Frame]' not found.
> Error: Data set with name 'proj[Frame]' not found.
> 'proj[Frame]': Invalid command or expression.
> > proj:1
> Warning: Data set 'proj:1' not found.
> Error: Data set with name 'proj:1' not found.
> 'proj:1': Invalid command or expression.
> > proj[kde_00026]
> Warning: Data set 'proj[kde_00026]' not found.
> Error: Data set with name 'proj[kde_00026]' not found.
> 'proj[kde_00026]': Invalid command or expression.
What am I doing wrong? Is what I am trying to accomplish not possible with cpptraj?
Thanks for any help on this,
Juan Eiros
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Received on Tue Apr 19 2016 - 05:00:05 PDT
