[AMBER] cpptraj: dihcovar and projection need trajin to work properly? - FollowUp

From: Thomas Fox <thomas_fox.gmx.net>
Date: Tue, 28 Feb 2017 16:42:48 +0100

   Ah, just realized the follwoing: if I read in a single frame, cpptraj runs
   through, but the covariance matrix consists of all zeros.
   I seemingly need the same number of frames in trajin as are in the dihedral
   data set.


   Gesendet: Dienstag, 28. Februar 2017 um 16:33 Uhr
   Von: "Thomas Fox" <thomas_fox.gmx.net>
   An: amber.ambermd.org
   Betreff: [AMBER] cpptraj: dihcovar and projection need trajin to work
   I found a cpptraj behavior that I think is at least unintuitive:
   From a previous cpptraj run, I have a data set of dihedrals which I would
   like to further process in a separate cpptraj run.
   So I use the "readdata" and "dataset mode torsion" commands followed by
   "matrix dihcovar dihedrals".
   However, unless I have read in a structure with trajin before (a single
   frame is enough, no matter how large my data set is),
   the size of the resulting matrix is 0.
   I find this weird, as I dont need the parm or trajin info - I exclusively
   work on the data set I got from readdata.
   The same is true for the projection command...
   Ah, and this occurs both with Amber16 cpptraj and with the (current?)
   cpptraj (it says version V17.00b) I got from github.
   I have attached my cpptraj input file as well as the dihedral data file and
   the output files for the two cases.
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Received on Tue Feb 28 2017 - 08:00:04 PST
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