Recover high precision coordinates from binary .coor file

From: Rajan Vatassery (
Date: Fri Nov 05 2010 - 19:37:48 CDT

        I'm looking for a way to somehow recover the double precision values
produced by NAMD's output function. Setting the binaryoutput to "no" in
the conf file produces a nice pdb file (a .coor file actually), but I
need a few more significant digits after the decimal. The manual says
that the binary output is double precision in terms of the coordinates
and I would like to view them in human-readable format.
        I have tried opening the binary output file with various binary
readers, but it's just a bunch of neatly spaced numbers of this type:

0000000 0064 0000 0000 0000 0000 0000 0000 0000
0000010 0000 0000 0000 0000 0000 0000 abd0 12a4
0000020 dbaf 3ffc c609 e22f bb90 3fd2 14af aa11
0000030 5884 3ffb 83a0 7d3c 104c 3fe0 b050 44fe
0000040 f0fb bfd3 ee29 7203 7319 4003 3728 2570
0000050 40dd bfe0 f690 cea8 718c 3fd6 77ea 5d27
0000060 65a7 c003 2ecd a69d b5c3 3ff3 cb72 81bc
0000070 4a90 3ffd a356 13d8 de8b 3ff2 caa1 114f
---- clipped very long file here --------------

and so on. The above was produced by the linux command hexdump, which
clearly outputs data in hex format. Unfortunately, I don't have any
experience in this field.
        I'll also add that I need to obtain coordinates for thousands of atoms
in hundreds of files, so batch scripting tips are much appreciated. Any
other help is, of course, appreciated as well. Thanks in advance,


Rajan Vatassery
Department of Chemistry
University of Minnesota

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