Molecular Modeling of Bifunctional Chelate Peptide Conjugates. 1. Copper and Indium Parameters for the AMBER Force Field
journal contributionposted on 28.08.2001, 00:00 by David E. Reichert, Per-Ola Norrby, Michael J. Welch
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.