[gmx-users] grompp or parameter file problem?

[Monika Sharma]

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 <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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>
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