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.ND2 :459.C1 :459.C2 :459.N2 chi1.csv
dihedral chi2 :298.CB :298.CG :298.ND2 :459.C1 chi2.csv
dihedral phin :298.CG :298.ND2 :459.C1 :459.H1 phin.csv
dihedral phi1 :460.H1 :460.C1 :459.O3 :459.C3 phi1.csv
dihedral psi1 :460.C1 :459.O3 :459.C3 :459.H3 psi1.csv
dihedral phi2 :461.H1 :461.C1 :460.O4 :460.C4 phi2.csv
dihedral psi2 :461.C1 :460.O4 :460.C4 :460.H4 psi2.csv
dihedral phi3 :462.H1 :462.C1 :461.O4 :461.C4 phi3.csv
dihedral psi3 :462.C1 :461.O4 :461.C4 :461.H4 psi3.csv
dihedral phi4 :463.H1 :463.C1 :462.O4 :462.C4 phi4.csv
dihedral psi4 :463.C1 :462.O4 :462.C4 :462.H4 psi4.csv
dihedral phi5 :464.H1 :464.C1 :463.O4 :463.C4 phi5.csv
dihedral psi5 :464.C1 :463.O4 :463.C4 :463.H4 psi5.csv
dihedral phi6 :465.H1 :465.C1 :462.O3 :462.C3 phi6.csv
dihedral psi6 :465.C1 :462.O3 :462.C3 :462.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
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Oct 15 2006 - 06:07:02 PDT
