[gmx-users] grompp or parameter file problem?

[Monika Sharma]

Hello Anna,
Did you checked your .gro file for the representation of atoms for water 
molecules and the itp files? I mean the atoms may be represented 
differently, that sometimes cause problem, even in my case that seemed 
to be problem. And one thing more does your system have its structure 
water molecules also? Do check their representation also...
Cheers..
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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