Re: AMBER: ptraj

From: Thomas E. Cheatham, III <>
Date: Mon, 12 Apr 2004 14:23:12 -0600 (Mountain Daylight Time)

> 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?

This does not sound like the correct behavior.

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

Better would be to grab the standard error information in the output file
as well...

  ptraj file.prmtop < >& ptraj.out

> trajin traj_all.crd.gz
> reference pfmrk_md_prod_ct6.rst.gz

It may be hanging on this reference command.

> trajout traj_all_image_NOWAT.crd

You probably want to specify "nobox" on the above line if you are
stripping water (otherwise you will have to build a prmtop with box
information but no water in order to continue with the stripped

> center:1-308 mass origin

There should be a space before the :1-308 above.

> image origin center
> rms first out rms_image_first.out: 1-308.CA
> rms reference out rms_image_last.out: 1-308.CA
> strip:WAT

There should be a space before the :WAT

I would try (1) adding the spaces before the : in each case
(2) Remove the references/ rms reference by commenting those lines out
(with a #) and (0) try processing only one frame first

trajin traj_all.crd.gz 1 1 1

It should run quick and I have run much larger systems without problem.

Good luck,

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy, Depts of
| Medicinal Chemistry and of Pharmaceutics and Pharmaceutical Chemistry
| Adjunct Asst Prof of Bioengineering; Center for High Performance Computing
| University of Utah, 30 South 2000 East, Skaggs 201, Salt Lake City, UT 84112
| (801) 587-9652; FAX: (801) 585-9119
\ BPRP295A / INSCC 418

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Received on Mon Apr 12 2004 - 21:53:00 PDT
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