AMBER Archive (2004)

Subject: Re: AMBER: ptraj

From: ayongye_at_sunchem.chem.uga.edu
Date: Tue Apr 13 2004 - 10:48:54 CDT

> 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_at_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_at_CA
should look thus:
     rms first out rms_image_first.out :1-308_at_CA
ie a space between the ouput file and the atom mask specification.
> #rms reference out rms_image_last.out: 1-308_at_CA
> strip :WAT

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