AMBER Archive (2004)

Subject: Re: AMBER: Amber

From: Thomas E. Cheatham, III (
Date: Tue Sep 28 2004 - 14:37:25 CDT

> PTRAJ: distance out model1-3-md1-dist1.dist time 0.1 :84_at_ND2 :197_at_O
> WARNING: Error in mask string, no "@" or ":" present (model1-3-md1-dist1.dist)

I forgot to mention that you need to give every distinct distance, bond,
angle, or dihedral command a unique identifier; this allows the results to
be saved and analyzed later... So the command should be

distance d1 out model1-3-md1-dist1.dist time 0.1 :84_at_ND2 :197_at_O

As originally written, "out" is assumed to be the unique identifier (and
stripped from the command line) so that "model1" becomes the first mask
and therefore fails... So, insert a name like "d1" right after the
distance keyword.

Good luck.

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