[gmx-users] grompp or parameter file problem?

[Yang Ye]

On 6/21/2007 6:20 PM, Anna Reymer wrote:
> 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!
then you shall only put a path after -I, instead of the file name.
>
> regards
> /anna
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