Re: AMBER: ptraj

From: <>
Date: Tue, 13 Apr 2004 11:48:54 -0400 (EDT)

> Dr. Cheatham,
> FOllowing your suggestion, I did ptraj again. Even for a single frame,
> ptraj has been running for 30m and hasn't fininshed. Is is normal?

It's not uncommon to have ptraj run for long periods of time, depending on
the size of your co-ordinate file.

> The trajectory file traj_all.crd is a combined one by using ptraj.
> Thanks for your help,
> Youyi
> Input file:
> trajin traj_all.crd 1 1 1
> #reference pfmrk_md_prod_ct6.rst.gz
> trajout traj_test.crd nobox
> center :1-308 mass origin
> image origin center
> rms first out rms_image_first.out: 1-308.CA

Looks like you did not apply one of Dr. Cheatham's recommendations. The
line above ie
     rms first out rms_image_first.out: 1-308.CA
should look thus:
     rms first out rms_image_first.out :1-308.CA
ie a space between the ouput file and the atom mask specification.
> #rms reference out rms_image_last.out: 1-308.CA
> strip :WAT

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Received on Tue Apr 13 2004 - 17:53:00 PDT
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