AMBER Archive (2006)

Subject: AMBER: Ptraj problems

From: Charlisa Daniels (charlisa.daniels_at_gmail.com)
Date: Thu Oct 12 2006 - 15:01:30 CDT

I am trying to analyze some trajectories and am having trouble getting ptraj
to read them. This is the script I use:

trajin peb3_bacil_MD.crd
trajin peb3_bacil_MDrst.crd

strip :WAT
strip :Cl-

rms first out rmsd.csv @CA

dihedral chi1 :298_at_ND2 :459_at_C1 :459_at_C2 :459_at_N2 chi1.csv
dihedral chi2 :298_at_CB :298_at_CG :298_at_ND2 :459_at_C1 chi2.csv

dihedral phin :298_at_CG :298_at_ND2 :459_at_C1 :459_at_H1 phin.csv

dihedral phi1 :460_at_H1 :460_at_C1 :459_at_O3 :459_at_C3 phi1.csv
dihedral psi1 :460_at_C1 :459_at_O3 :459_at_C3 :459_at_H3 psi1.csv

dihedral phi2 :461_at_H1 :461_at_C1 :460_at_O4 :460_at_C4 phi2.csv
dihedral psi2 :461_at_C1 :460_at_O4 :460_at_C4 :460_at_H4 psi2.csv

dihedral phi3 :462_at_H1 :462_at_C1 :461_at_O4 :461_at_C4 phi3.csv
dihedral psi3 :462_at_C1 :461_at_O4 :461_at_C4 :461_at_H4 psi3.csv

dihedral phi4 :463_at_H1 :463_at_C1 :462_at_O4 :462_at_C4 phi4.csv
dihedral psi4 :463_at_C1 :462_at_O4 :462_at_C4 :462_at_H4 psi4.csv

dihedral phi5 :464_at_H1 :464_at_C1 :463_at_O4 :463_at_C4 phi5.csv
dihedral psi5 :464_at_C1 :463_at_O4 :463_at_C4 :463_at_H4 psi5.csv

dihedral phi6 :465_at_H1 :465_at_C1 :462_at_O3 :462_at_C3 phi6.csv
dihedral psi6 :465_at_C1 :462_at_O3 :462_at_C3 :462_at_H3 psi6.csv

trajout peb3_bacil_MD_nowat.crd
go

And this is the error message I get:
PTRAJ: trajin peb3_bacil_MD.crd
WARNING in checkCoordinates(): Could not open file (peb3_bacil_MD.crd)
WARNING in ptrajSetupIO(): trajin peb3_bacil_MD.crd, cannot open file...

PTRAJ: trajin peb3_bacil_MDrst.crd
WARNING in checkCoordinates(): Could not open file (peb3_bacil_MDrst.crd)
WARNING in ptrajSetupIO(): trajin peb3_bacil_MDrst.crd, cannot open file...

I have checked the file permissions and for typos and everything else that
has been conjectured as a possible culprit on the AMBER archive, but
nothing helps. Does anyone else have an inkling?

    Charlisa Daniels

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