[gmx-users] current directory files

[Mark Abraham]

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 <mailto: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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