On 6/20/07, Mark Abraham <[EMAIL PROTECTED]> 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!
regards
/anna
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