Date: Fri, 26 Jul 2002 12:15:04 -0700 (PDT)
From: Thomas Cheatham
Subject: RE: ptraj


Yes, you are both stumbling upon little ptraj issues that I should clean
up and clear up...

> "Set #21 is corrupted" and quote the last three coordinates of set 20 (which

This is a problem with the current implementation in that the program does
not differentiate between the "end" of a trajectory and its corruption nor
its truncation. The (anachronistic) comment is meant as a warning; in
the case of Joseph Nachman's frame 101 corruption, since you know you had
100 frames, don't worry about frame 101; the results should be fine up to
101 or wherever that message came up.

I will fix this to:

(1) Differentiate between a truncated frame/snapshot, actual
corruption of the trajectory (such as *'s in output), and regular end
of file.
(2) Make the end of file message seem less ominous :-)


> I found out (the hard way) that the flag "nobox" is critical for outputting

This is another little annoying issue that burns me all the time too
believe it or not. By default, box information is output to the output
trajectory UNLESS the nobox keyword is specified. I need to make this a
little smarter to NOT output box information for invacuo/continuum runs
(i.e. if no box info was initially present or specified, don't output box
information!).

...and finally, I agree that the ptraj manual is a little sparse and I
will work to improve it.

Thanks for pointing out the issues and also, in general, for the helpful
replies of AMBER/ptraj users to the list!