AMBER Archive (2005)

Subject: AMBER: Fail to load the trajectory file.

From: Jinzhi Lei (jzlei_at_mail.tsinghua.edu.cn)
Date: Mon Apr 11 2005 - 19:36:34 CDT

Hi, all,

I have problem while I use ptraj to load the trajectory file hd5_wat.md.crd. The output is given below. It is supposed that the file is too large (about 2GB). I would like to know can I treat this file by ptraj. Or can I split it into several smaller files? Thanks.

Jinzhi

Here is the output when I run the ptraj:

...
Initializing state: detected PBC beta angle in prmtop that is not 90.0!
Assuming this box is a truncated octahedron, angle is 109.471221

PTRAJ: Processing input file...
       Input is from file traj.in

PTRAJ: trajin hd5_wat.md.crd
Checking coordinates: hd5_wat.md.crd

Could not open file (hd5_wat.md.crd) with mode (r)
WARNING in checkCoordinates(): Could not open file (hd5_wat.md.crd)
WARNING in ptrajSetupIO(): trajin hd5_wat.md.crd, cannot open file...

PTRAJ: trajout traj/hd5.traj pdb
WARNING in ptraj(): No input trajectories specified (trajin),
aborting...

***************************************************************
+ Jinzhi Lei
+ Zhou Peiyuan Center for Applied Mathematics,
+ Tsinghua University, Beijing, China, 100084
+
+ Department of Mathematics,
+ University of California, Irvine,
+ CA 92697-3875
+
+ Email: jzlei_at_mail.tsinghua.edu.cn
+ jzlei_at_math.uci.edu
+ URL: http://zcam.tsinghua.edu.cn/~jzlei
**************************************************************

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