cofactors topology and parameters were retrieved from:

http://research.bmh.manchester.ac.uk/bryce/amber

Related reference:

HEME: Giammona, DA [Ph.D. thesis, University of California, Davis (1984)]
ATP: Meagher KL, Redman LT, Carlson HA [Journal of Computational Chemistry           2003,24,1016 - "Development of polyphosphate parameters for use with the        AMBER force field" ]

ADP, AMP: by analogy from ATP

NADH: U. Ryde [ Proteins, Struct. Funct. Genet. 21(1995)40-50 - "Molecular            dynamic simulations of alcohol dehydrogenase with varying coordination          number of the catalytic zinc ion"]
NAD+: U. Ryde [ Prot. Sci. 4(1995)1124-1132 - "On the role of Glu-68 in alcohol       dehydrogenase" ]

NADP: N. Holmberg, U. Ryde, and L. Bulow [ Prot. Engin., 12 (1999) 851-856. -
      "Redesign of the coenzyme specificity in L-lactate dehydrogenase from            Bacillus stearothermophilus using site-directed mutagenesis and media           engineering."]

GDP, GTP: Meagher KL, Redman LT, Carlson HA [ Journal of Computational Chemistry 2003,24,1016 - "Development of polyphosphate parameters for use with the AMBER force field" ]

FMN : Schneider C, Suhnel J [Biopolymers 1999,50,287 "A molecular dynamics simulation of the flavin mononucleotide-RNA aptamer complex" ]
