crd file input for ptraj

From: Michael Cooney <mike_at_bmbiris.bmb.uga.edu>
Date: Tue 12 Dec 2000 12:02:37 -0500 (EST)

Dear Amber users,

I have been trying to process a molecular dynamics crd file using ptraj to
center the solute within the box after the dynamics run. The problem is
that ptraj does not seem to like g-zipped files (.gz extension). Here is
the input file:
trajin pme2_prod.crd
trajout pme2_centered.traj
center
image
go

..and the error from the output:

PTRAJ: trajin pme2_prod.crd

Could not open file (pme2_prod.crd) with mode (r)
WARNING in checkCoordinates(): Could not open file (pme2_prod.crd)
WARNING in ptrajSetupIO(): trajin pme2_prod.crd, cannot open file...

A similar error occurs if I try to use a .gz file; the program says
"Could not open file (pme2_prod.crd.Z)". Does ptraj expect conventionally
compressed files (.Z)?

Thanks for any help.

Sincerely,

Michael Cooney
Dept. of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602
Received on Tue Dec 12 2000 - 09:02:37 PST