[gmx-users] grompp problems
Mark.Abraham at anu.edu.au
Wed Oct 4 03:32:14 CEST 2006
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
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 :-)
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