Hello Anna,
One thing. It is that the topology file includes in solvent topology
section is tip3p.itp, but you are using amber99. Is it same as
ffamber_tip3p.itp. If not, then i think you can try changing it to
ffamber_tip3p.itp..
Hope it helps..
Monika
Yang Ye wrote:
On 6/21/2007 6:20 PM, Anna Reymer wrote:
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!
then you shall only put a path after -I, instead of the file name.
regards
/anna
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