On Sep 9, 2008, at 2:53 AM, David van der Spoel wrote:
Christopher Daub wrote:
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.
grompp uses a temporary file and for the the environment variable
$TMPDIR is read. Is that pointing to /grace/bin ?
Thanks a lot for the suggestion. This variable is not set. I tried
to set it to the current directory (export TMPDIR=./), but it didn't
make a difference. Where is this set? I grep'd for TMPDIR in the src/
kernel directory and couldn't find any reference to it... are you
sure this is right? Maybe there's another variable getting set
somewhere... is there a list somewhere of environment variables used
by gromacs?
I tried other preprocessors other than the default cpp (m4, and a
cpp.ansi I found in /usr/lib) but get the same error... so it does
seem to be grompp, not the cpp...
Cheers,
Chris.
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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--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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