Molecular modeling of bifunctional chelate peptide conjugates. 1. Copper and indium parameters for the AMBER force field.

In this work we describe the development of parameters for In(III) and Cu(II) for the AMBER force field as found in the modeling package MacroModel. These parameters were developed using automated procedures from a combination of crystallographic structures and ab initio calculations. The new parameters were added in the form of AMBER substructures containing specific metal-ligand parameters to the existing force field. These new parameters have produced results in good agreement with experiment without requiring additional changes to the existing AMBER parameters. These parameters were then utilized to examine the conformational effects caused by the conjugation of InDTPA (DTPA = diethylenetriaminepentaacetic acid) and CuDOTA (DOTA = 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) to the cyclic octapeptide octreotide.