[gmx-users] fatal error grompp !

Mark Abraham Mark.Abraham at anu.edu.au
Mon May 21 21:15:04 CEST 2007

Philippe Reymond wrote:
> Dear Gromacs Users, 
> I just installed Gromacs on my windows
> machine (with a gromacs especially for Windows XPdownloaded) from your
> website.
> Everything seemed to go fine with the installation and there
> is no problem when I execute pdb2gmx, editconf and genbox.
> But, when
> I execute grompp, I get this error :
> ...
> creating
> statusfile for 1 node...
> Warning: as of GMX v 2.0 unit of
> compressibility is truly 1/bar
> checking input for internal
> consistency...
> calling cpp...
> cpp: Files\Gromacs\share\top: No
> such file or directory
> cpp exit code: 33
> Tried to execute:
> 'cpp  -IC:\Program Files\Gromacs\share\top -DFLEX_SPC
> 1TW7_initiale.top > gromppa00684'
> The 'cpp' command is defined in
> the .mdp file
> processing topology...

Here's the problem. grompp calls your cpp with an include directory (the 
  -I flag) that has a space in it. You can see this is the problem in 
the line after "calling cpp..." since cpp doesn't understand what comes 
after the space.

The quickest work-around is to put gromacs in a folder with no space in 
the filename. Then fix the environment variables.

More generally effective and certain to lead to less heartache in the 
long run is to install Cygwin and following my HOWTO on installing 
Gromacs under Cygwin. Now you have a full Unix compatibility layer and 
can re-use all of the existing collective knowledge base of using 
Gromacs under Unix, instead of finding new corners on the wheel to 
"bounce over" all the time.


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