[gmx-users] current directory files

[Mark Abraham]

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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