AMBER Archive (2000)

Subject: crd file input for ptraj

From: Michael Cooney (mike_at_bmbiris.bmb.uga.edu)
Date: Tue Dec 12 2000 - 11:02:37 CST

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