Hey again!
The install of gromacs 3.3.3 on HP-UX is mostly working fine, but I'm
getting some weird behaviour from grompp where it doesn't set the
output filename correctly. Here is the grompp output from when I run
the demo program, for example (the demo works fine until it gets to
this step, after pdb2gmx and genbox):
------------------------------------------------------------------------
----
checking input for internal consistency...
sh: /grace/bin/: Cannot create the specified file.
Cleaning up temporary file gromppa11751
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: topio.c, line: 312
Fatal error:
Could not open /grace/bin/
-------------------------------------------------------
"If Life Seems Jolly Rotten, There's Something You've
Forgotten !" (Monty Python
)
:-) G R O M A C S (-:
GRoups of Organic Molecules in ACtion for Science
:-) VERSION 3.3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and
others.
Copyright (c) 1991-2000, University of Groningen, The
Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) grompp (-:
creating statusfile for 1 node...
calling /usr/bin/cpp...
cpp exit code: 256
Tried to execute: '/usr/local/bin/cpp -I/home/snoop/gmacs/share/
gromacs/top -DFLEX_SP
C cpeptide.top > /grace/bin/'
The '/usr/bin/cpp' command is defined in the .mdp file
processing topology...
---------------------------------------------------------
I think it's getting the /grace/bin thing from my PATH variable of
all things! Why it sticks it in there as the output filename is
beyond me. I've looked at grompp.c and topio.c to see if I can find
the problem, but my C coding skills are not great and I'm not sure
what to do with all those pointers... can anyone suggest an easy fix
for this? I tried an ugly hack to set outfile = "cppoutput" in
topio.c, but that didn't work...
Thanks for any suggestions (other than getting rid of HP-UX...),
Chris.
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