FF.dat

The FF.dat file contains a list of the force fields supported by GROMACS, from which you choose when prompted by pdb2gmx.  To introduce a new force field into GROMACS (i.e., in the case of adding the ffamber ports), you need to add entries to this file, and increment the counter on the first line before pdb2gmx will recognize it.  As of GROMACS version 4.0, the contents of FF.dat are:

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ffG43a1    GROMOS96 43a1 force field
ffG43a2    GROMOS96 43a2 force field (improved alkane dihedrals)
ffG45a3    GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
ffG53a5    GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
ffG53a6    GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
ffoplsaa   OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
ffgmx      [DEPRECATED] Gromacs force field (see manual)
ffgmx2     [DEPRECATED] Gromacs force field with hydrogens for NMR
ffencadv   Encad all-atom force field, using scaled-down vacuum charges
ffencads   Encad all-atom force field, using full solvent charges