[gmx-users] grompp or parameter file problem?

Anna Reymer anna.reymer at gmail.com
Thu Jun 21 12:20:10 CEST 2007

On 6/20/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Anna Reymer wrote:
> > Hello all!
> >
> > I am trying to simulate DNA dodecamer in TIP3P water with Amber 99 port.
> > I was ablle to produce dna+solvent.top (attached file) and dna+solvent.gro.
> > When running grompp:
> >
> > grompp -f em.mdp -c dna+solvent.gro -p dna+solvent.top -o out.tpr
> >
> > with the following em.mdp:
> > -------------------------------------
> > ;       DNA energy minimization in water
> > ;
> > cpp             = /lib/cpp -traditional
> > define          =
> > include         = -I/***/share/gromacs/top/ffamber99.itp
> This is not the right approach, but might not be the cause of the
> problem. Your .top should #include this file itself (see
> http://wiki.gromacs.org/index.php/include_file_mechanism). This -I flag
> provides an alternate path search in looking for this file. The three
> asterixes are weird... use the correct path, and make it a path, not a file.
> Mark

Hi Mark!
The tree asterixes is just the path to my folder. The path is quite
long and I substituted it in the mail by three asterixes in the file
it is a normal 100 letters path.
My top file included the file itself and I tried to provide a path to
top directory not only to a special file, but neither path to the top
directory no path to file did not provide any good changes.

Thank you very much for your help!


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