I'm forwarding this to Wes for a look ...
Ray
---------- Forwarded message ----------
From: Jan-Philip Gehrcke <jgehrcke.googlemail.com>
Date: Mon, Jun 25, 2012 at 10:33 AM
Subject: [AMBER] AmberTools 12 pbsa: missing newline character in OpenDX
output
To: AMBER Mailing List <amber.ambermd.org>
Hello,
there seems to be a small problem in the OpenDX-file-writing-feature of
pbsa in AmberTools 12. If the number of grid points is not an integer
multiple of 3, a missing newline character in the footer of the file
violates the format specification. These are the last few lines of a
problematic DX file written by pbsa:
1.3079431969E+01 1.2508119413E+01 1.1935395284E+01
1.1363278074E+01 1.0795899087E+01 1.0246391314E+01
9.7028066689E+00 9.1626945187E+00 8.6272002140E+00
8.1016960668E+00 attribute "dep" string "positions"
object "Electrostatic Potential" class field
component "positions" value 1
component "connections" value 2
component "data" value 3
There has to be a newline character before "attribute", according to
http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data
VMD emits an error on attempting to load such a file. With the newline
character, VMD loads the file properly.
Regards,
Jan-Philip Gehrcke
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Received on Mon Jun 25 2012 - 11:00:03 PDT
