Hi Jack,
If you have AMBER you can define new residues pretty easily
especially since you already have charges you like. Once you have a
topology and coordinate file, "ambpdb -pqr -wrap -p FILE.top < FILE.crd >
FILE.pqr" will generate a MEAD style pqr file.
Richard
--
Jack,
Editing the output PQR sounds like a sensible approach.
As far as obtaining charges goes: in order to be quantitatively correct, the
ligand would need to be parameterized using the same approach as the protein
force field...(for Amber99, I think that means performing an ab initio
quantum
