AMBER Archive (2002)

Subject: RE: ptraj

From: Thomas Cheatham (cheatham_at_chpc.utah.edu)
Date: Fri Jul 26 2002 - 14:15:04 CDT

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!

\ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
| Departments of Medicinal Chemistry and of University of Utah
| Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East, Room 201
| & Center for High Performance Computing Salt Lake City, Utah 84112
|
| e-mail: tec3_at_utah.edu phone: (801) 587-9652 FAX: (801) 585-9119
\ http://www.chpc.utah.edu/~cheatham Offices: BPRP295A / INSCC 418