[gmx-users] costu, fragment force field

[nemethl at pharm.u-szeged.hu]

I'm attempting to build a costume fragment library of beta amino acids
with GAFF parametrization. I have converted the AMBER assigned parameters
with acpype, built my .rtp .atp and .itp files. Everything works fine,
until grompp, there i get a lot of "No default Ryckaert-Bell. types"
errors. The problem is, that the dihedrals in question are mentioned in
the ffbonded.itp file, but the atomtypes are not in good order. How do i
figure out the RB parameters for these bonds, in the precise order? Is
there a way to convert the parameters to the desired order?

Thank you in advance!

Lukacs Nemeth