[gmx-users] grompp cpp pre-processor

[David]

On Mon, 2005-06-06 at 15:10 -0500, Nathan Moore wrote:
> 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!
> 
remove the whole line from the mdp file or change it to
cpp = cpp
(works whenever cpp is in your path). We should change the default...
> NT Moore
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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