[gmx-users] grompp or parameter file problem?

[Mark Abraham]

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