From amber to gromacs

There is a useful tool to use amber potential in gromacs.

http://chemistry.csulb.edu/ffamber/

There some changes might need to apply before using a pdb file with pdb2gmx program. For exmaple, we build a peptide with sequence (use amber03 force field)

NARG ARG GLU GLU TRP TRP ASP ASP ARG ARG GLU GLU TRP TRP ASP CASP

The atom types in the pdb file are slightly different from that listed in ffamber (ffamber03.rtp):

AMBER ffamber

...

N --- N
H --- H
CA --- CA
HA --- HA
CB --- CB
2HB --- HB1
3HB --- HB2
CG --- CG
OD1 --- OD1
OD2 --- OD2
C --- C
O --- O

...

So we need to rename "2HB" and "3HB" to "HB1" and "HB2", Similarly we need to the following:

2HB -> HB1

3HB -> HB2

2HG -> HG1

3HG -> HG2

1HH1 -> HH11

2HH1 -> HH12

1HH2 -> HH21

2HH2 -> HH22

2HD -> HD1

3HD -> HD2

...

The following bash script can be used to process such a pdb file.

http://docs.google.com/Doc?id=dfvdq4zs_161ctvzp2gx

We also have to rename the first residue name from "ARG" to "NARG", and the last residue name from "ASP" to CASP.