[gmx-users] current directory files

[tarak karmakar]

Thanks a lot........now it's working....:)

On Fri, Jun 15, 2012 at 2:00 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 15/06/2012 6:21 PM, tarak karmakar wrote:
>
> Hi,
>
>   Thanks for the reply.
> One thing, while giving the '-ff' flag it is asking for some string. So I
> renamed all my force field files as except spc.itp and ions.itp. Renamed
> files are .....
>
> 1) ffprot.atp
> 2) ffprot.rtp
> 3) ffprot.itp [ includes ffnonbonded.itp and ffbonded.itp ]
>
> pdb2gmx -f test.pdb -o test.gro -p toplo.top -ff prot
>
> so it'll read all of these files starting with 'ff'
> Then how can I deal with spc.itp and ions.itp files ?? Should I include
> the scp.itp and ions.itp files inside the ffprot,itp ??
>
>  On Fri, Jun 15, 2012 at 12:50 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
>
>>
>>  You need the kind of approach described here
>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>>
>>
> You started with files from some force field. Copy the whole folder, like
> it says in the above link. Then modify the files there...
>
> Mark
>
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-- 
*Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
Ph. (lab) : +91-80-22082809 *
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