[gmx-users] fatal error grompp !

Philippe Reymond philippe.reymond at u-psud.fr
Mon May 21 19:54:31 CEST 2007

Dear Gromacs Users, 

I just installed Gromacs on my windows
machine (with a gromacs especially for Windows XPdownloaded) from your
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 :

statusfile for 1 node...
Warning: as of GMX v 2.0 unit of
compressibility is truly 1/bar
checking input for internal
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...
Fatal error: number of coordinates in coordinate file
(1TW7_boite_eau.gro, 14299)
does not match topology
(1TW7_initiale.top, 0)

C:\Documents and

that, the process stops and the content of the topology file is removed
(the file made 0 KB).

How to solve this problem ? Can you say
to me clearly and simply how to make?

You must know that :

* Gromacs was installed in the C:\Program Files\Gromacs file
* Variable Environment path was modified to specify the way of the
directory (C:\Program Files\Gromacs\bin)
* A new variable
Environment was created, called GMXLIB showing the way of the forcefields
Gromacs (C:\Program Field\Gromacs\share\top)
* In the .mdp file, cpp
was defined as C:\Program Files\bin\cpp (before it was /lib/cpp)
cpp.exe really exists in this directory and have a size of 87 Ko
* My
computer is an IBM, Windows Xp SP2, Intel Pentium M 1.73 GHz, 504 Mo of

Thank you very munch for your help !

Université Paris Sud
Faculté des Sciences
philippe.reymond at u-psud.fr 

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