Good morning,
I am attempting to perform a principle component analysis but am
encountering an unexpected error during the projection step using cpptraj:
Error: number selected coords (5865) != number avg coords (10983) in myEvecs
In short, I am confused how a mismatch could occur. My understanding is
that if my eigenvectors (myEvecs) come directly from the covariance
matrix of a given trajectory, no mismatch should be possible (if I have
consistent masks). I must be confused and seek clarification.
I am using cpptraj v. 15. I am following the tutorial specified on
http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/
My cpptraj commands are (in blue), with trivial warning messages listed
(in red):
trajin full_no_waters.mdcrd
reference Crystal_Structure_with_Hydrogens.pdb
Warning: PDB line length is short (67 chars, expected 80).
Warning: PDB Crystal_Structure_with_Hydrogens.pdb: Reading frame 2, got
711 atoms, expected 4431.
Warning: Only using frames 1-1
createcrd full_no_waters.mdcrd
run
crdaction full_no_waters.mdcrd rms ref
Crystal_Structure_with_Hydrogens.pdb :38-318&!.H
Warning: Coordinates are being rotated and box coordinates are present.
Warning: Unit cell vectors are NOT rotated; imaging will not be possible
Warning: after the RMS-fit is performed.
crdaction full_no_waters.mdcrd matrix covar name full_no_waters_covar
:38-318&!.H
runanalysis diagmatrix full_no_waters_covar out full_no_waters_evecs.dat
vecs 3 name myEvecs nmwiz nmwizvecs 3 nmwizfile protein.nmd nmwizmask
:38-318&!.H
Up to this point, the warnings listed are trivial and everything seems
fine. I then give the command
crdaction full_no_waters.mdcrd projection full_no_waters_projection3
modes myEvecs beg 1 end 3 :38-318&!.H=
Error: number selected coords (5865) != number avg coords (10983) in myEvecs
--
Dr. Robert Molt Jr.
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Received on Sat Aug 11 2018 - 22:30:03 PDT
