[gmx-users] How to use AMBER99sb and GAFF force fields for different parts of ONE molecule?

[Thomas Schlesier]

Dear all,

I have found that the GAFF force field is used in concert with the AMBER 
fore fields. Since both force fields use the same [ defaults ] section 
in the forcefield.itp files, I think GROMACS can come up with nonbonded 
parameters between these force field.
But since both force fields use different names for the atomtypes, I 
have no idea how GROMACS could come up with bonded parameters between 
both force fields (I want to describe a dye molecule attached to a RNA 
molecule).
Any ideas?

Greetings
Thomas