[gmx-users] current directory files

tarak karmakar tarak20489 at gmail.com
Fri Jun 15 08:27:10 CEST 2012

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 ?
Thanks in advance.........

*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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