Hi,
What version of cpptraj are you using? I believe the 'crdset' keyword
of 'average' requires at least AT 15.
-Dan
On Mon, Jul 10, 2017 at 6:07 AM, Ramin Salimi <ramin.salimi01.utrgv.edu> wrote:
> Dear All
>
> I am trying to diagonalize my mass-weighted covariance matrix with the following script in cpptraj:
>
> parm strip.49.0.mbondi3.prmtop
> trajin strippedtraj.49.0.crd
> rms first :1-24&!.H=
> average crdset 49.0.average
> run
> readdata 49.0.average
> rms ref 49.0.average :1-24&!.H=
> matrix mwcovar name 49.0.mwcvmat :1-24&!.H= out mwcvmat.49.0.dat
> createcrd 49.0.trajectories
> run
> runanalysis diagmatrix 49.0.mwcvmat out evecs.49.0.dat vecs 20 name myEvecs.49.0 nmwiz nmwizvecs 20 nmwizfile dna.49.0.nmd nmwizmask :1-24&!.H= thermo outthermo thermo.49.0.dat temp 300.0
>
> But I get the following error:
>
>
> Read 2000 frames and processed 2000 frames.
> TIME: Trajectory processing: 0.9064 s
> TIME: Avg. throughput= 2206.5362 frames / second.
>
> ACTION OUTPUT:
> AVERAGE: [crdset 49.0.average]
> Writing 'crdset' as Amber Trajectory
> 'crdset' is an AMBER trajectory, Parm strip.49.0.mbondi3.prmtop: Writing 2000 frames (1-Last, 1)
>
> DATASETS:
> 1 data set:
> RMSD_00000 "RMSD_00000" (double, rms), size is 2000
> ---------- RUN END ---------------------------------------------------
> [readdata 49.0.average]
> Error: File '49.0.average' does not exist.
> Error: Could not read data file.
> 1 errors encountered reading input.
> TIME: Total execution time: 0.9140 seconds.
>
> Why can't it save the average structure to use it as the reference for the next rms? I tried different ways of writing this script but all failed.
>
> I would appreciate if someone shares some insight on how to change it.
> Best Regards
> Ramin
>
>
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Mon Jul 10 2017 - 06:00:07 PDT
