[gmx-users] current directory files

[tarak karmakar]

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:

>  On 15/06/2012 4:27 PM, tarak karmakar wrote:
>
> Dear All,
>
>
>       In my protein pdb file I have changed some of the amino acid residue
> names. So accordingly I have changed corresponding residue names in force
> filed files and kept all the files [ modified and unmodified ] in my
> current working directory. Those files are
>
> 1) atomtypes.atp
> 2) aminoacids.rtp
> 3) ffnonbonded.itp
> 4) ffbonded.itp
> 5) spc.itp
> 6) ions.itp
>
> now while giving the command
> pdb2gmx -f prot.pdb -o prot.gro -p toplogy.top
>
> how can I make use of all these force field files present in my current
> working directory ?
>
>
> You need the kind of approach described here
> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>
> 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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