AMBER Archive (2007)

Subject: AMBER: Binary file curiosities

From: David LeBard (david.lebard_at_asu.edu)
Date: Fri Aug 03 2007 - 17:59:45 CDT

Hi Amber folks,

I have been playing with reading the various binary AMBER trajectory data
types lately, and I noticed a few things that strike me as puzzling
"features" of AMBER. For instance, from what I can tell from mdwrit.f, if
you choose the option NTRX=1 in sander you get an unformatted file that
looks exactly like the formatted mdcrd file. However, I do not see the
option to write these types of files from ptraj, only binpos binary files
are available (from my inspection of trajectory.c). Also, possibly due to
my lack of c expertise, I do not see the option to read binary mdcrd files
within ptraj itself. So my questions are the following: 1) Why such
inconsistencies with the binary file types across the various sander
modules? I understand that you must try to be as backward compatible as
possible, but consistency between file reads and writes would make things
much easier for the users (including myself). 2) Is the magic number in the
binpos file type only used only to determine the difference between binpos
and CHARMM trajectories? 3) Has anyone worked with reading binpos files in
fortran, particularly using direct access reads? If so, can you please
provide any examples? 4) Is there any documentation anywhere on the binpos
file type? I have been looking all over, and only believe I know what is in
the file because of the "od" command and code/comments inside ptraj.
Please, if I am missing an obvious reference to the binpos file structure,
do not hesitate to send it my way.

Thank you in advance for any help,
David LeBard

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