The Extended Zinc AMBER Force Field (EZAFF).

An empirical approach based on the previously developed zinc AMBER force field (ZAFF) is proposed for the determination of the parameters for bonds and angles involving zinc. We call it the extended ZAFF (EZAFF) model because the original ZAFF model was only formulated for 4-coordinated systems, while EZAFF additionally can tackle 5- and 6-coordinated systems. Tests were carried out for 6 metalloproteins and 5 organometallic compounds with different coordination spheres. Results validated the reliability of the current model to handle a variety of zinc containing complexes. Meanwhile, benchmark calculations were performed to assess the performance of 3 bonded molecular mechanics models (EZAFF, Seminario, and Z-matrix models), 4 nonbonded parameter sets (the HFE, IOD, CM and 12-6-4 models) and 4 semiempirical quantum mechanical methods (AM1, PM3, PM6 and SCC-DFTB methods) for simulating zinc containing systems. The obtained results indicate that, even with their increased computational cost, the semiempirical quantum methods only offered slightly better accuracy for the computation of relative energies and only afforded similar molecular geometries, when compared to the investigated molecular mechanics models.

Citation

Zhuoqin Yu, Pengfei Li, Kenneth M Merz. The Extended Zinc AMBER Force Field (EZAFF). Journal of chemical theory and computation. 2017 Nov 17

PMID: 29149560

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