[gmx-users] problem with porting excutables to another site (IBM AIX)

Ruhong Zhou ruhongz at us.ibm.com
Sun Apr 20 06:27:01 CEST 2003


I am having trouble when trying to port the compiled gromacs excutables to 
another site (a remote site). I changed PATHs in
GMXRC and GMARC.bash etc to proper new localtions, and the program pdb2gmx 
found the right location for top lib files, and it ran.
However, it core dumps at the end:


 3: GROMOS96 43b1 Vacuum Forcefield (official distribution)
 4: GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)
 5: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
Using ffoplsaa force field
Opening library file /dfs/protein/programs/gromacs/share/top/ffoplsaa.atp
Atomtype 696
Reading residue database... (ffoplsaa)
Opening library file /dfs/protein/programs/gromacs/share/top/ffoplsaa.rtp
Residue 50
Sorting it all out...
Opening library file /dfs/protein/programs/gromacs/share/top/ffoplsaa.hdb
Opening library file 
Opening library file 

Back Off! I just backed up 1a45.top to ./#1a45.top.3#
Processing chain 1 (1481 atoms, 173 residues)
Opening library file /dfs/protein/programs/gromacs/share/top/specbond.dat
5 out of 5 lines of specbond.dat converted succesfully
Illegal instruction (core dumped)

Am I missing something here? Do I have to do something else, or do I have 
to recompile/install in the new enviornment?The OS is the same, both are 
IBM AIX (IBM SP Power3 nodes)



Ruhong Zhou , PhD
Computaional Biology Center 
IBM Thomas J. Watson Research Center 
Yorktown Heights,  NY 10598 
Tel: (914) 945-3591, Fax: (914) 945-4104 
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