AMBER Archive (2004)

Subject: AMBER: ptraj

From: pengyo_at_UMDNJ.EDU
Date: Mon Apr 12 2004 - 15:09:22 CDT

Dear AMBER users,
I try to use ptraj to analyze my MD trajectory file, which is pretty big and
contains about 630 snapshots (one 308AA protein+9A water shell). Ptraj has
been running for 7531m and nothing is in the output file.Is this normal? I
guess something must be wrong. The program iniated normally and checked the
coordinates in the file "traj_all.crd.gz" and then stopped there.
Anybody has any idea?

The command I typed is "ptraj file.prmtop <ptraj.in> ptraj.out"

The traj.in is here:
trajin traj_all.crd.gz
reference pfmrk_md_prod_ct6.rst.gz
trajout traj_all_image_NOWAT.crd
center:1-308 mass origin
image origin center
rms first out rms_image_first.out: 1-308_at_CA
rms reference out rms_image_last.out: 1-308_at_CA
strip:WAT

 

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