[gmx-users] grompp cpp pre-processor

[Nathan Moore]

I've installed GROMACS on an apple laptop running os X.  I installed the
files, and making was simple this time.  I notice though that when I try
the demo or the benchmarks, GROMACS fails at the stage of creating an .mdp
binary for use in mdrun.

Specifically, when I look at the villin example from the benchmarks:


3:06pm|nmoore at winesap> ls
conf.gro  grompp.mdp  mdout.mdp  topol.top
3:06pm|nmoore at winesap> grompp -f grompp.mdp -p topol.top -c conf.gro -o
villin.tpr

...

calling /lib/cpp...
sh: line 1: /lib/cpp: No such file or directory
cpp exit code: 32512
Tried to execute: '/lib/cpp  -I/usr/local/gromacs/share/top  topol.top >
grompp9uh5Yn'
The '/lib/cpp' command is defined in the .mdp file
processing topology...
processing coordinates...
Fatal error: number of coordinates in coordinate file (conf.gro, 9389)
             does not match topology (topol.top, 0)

 - - -

Now I can certainly add in the location of cpp with an include flag,
3:07pm|nmoore at winesap> which cpp
/usr/bin/cpp

but is this the only problem (and if so, what's the proper flag?)?

the error "number of coordinates in coordinate file (conf.gro, 9389) does
not match topology (topol.top, 0)" makes no sense at all as toplo.top has
quite a bit of information within.

Any suggestions would be welcomed.  It is exciting to get the package
running!

NT Moore