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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Received on Mon Jul 10 2017 - 03:30:02 PDT
