[gmx-users] grompp problems

[Mark Abraham]

Ken Rotondi wrote:
> Hi all,
> 
> I'm having troubles with grompp.
> 
> Building .gro and .top files from a .pdb file of a 7 residue peptide (61 
> atoms in uaff) results in a system with  5137 atoms in the gro file and 
> a .top file with 1 protein (61 atoms) and 1692 solvent (5076 atoms). 
> When I ran grompp it fatal erred stating that the "number of coordinates 
> in the coordinate file (5137 atoms) does not match topology (0 atoms).

Sounds like you're not giving grompp a real .top file.

> My .mdp file had the default
> 
> cpp  =  /lib/cpp
> 
> so I ran the command; 'which cpp', which returned /usr/bin/cpp
> 
> I changed the .mdp to
> 
> cpp  =  /usr/bin/cpp
> 
> and I get the same error.

Yeah don't worry about that.

> If I run grompp with the -pp option the processed top file returned is 
> empty

That's consistent with not giving grompp a real .top file.

> Could this have something to do with the
> 
> include  =  -I../top
> 
> in the preprocessing section of the .mdp file? It would seem to be the 
> only thing left.

That just tells cpp some directories in which to look for the files 
#included in the .top file (see manual). Whether it's significant 
depends on the contents of your .top file. Hint, hint :-)

Mark