Chemistry, Department of
Date of this Version
Spring 4-28-2014
Citation
Hongbo Zhu, IMPLEMENTATION AND APPLICATION OF THE MMFF94 FORCE FIELD, MS thesis, University of Nebraska-Lincoln, 2014
Abstract
MMFF94 is implemented for molecular mechanics calculation in the quantum chemistry polarizable force field program (QuanPol). As a general force field for organic molecules, the availability of MMFF94 expends the capability of the QuanPol program. The MMFF94 force field atom type determination and parameter matching methods are established and corresponding program routines are written in the FORTRAN language. In this implementation, the MMFF94 atom types can be determined automatically from the connectivity of the input atoms with no or minimum information of formal charges. This implementation of MMFF94 is validated using the 761 standard tests, thus is a complete implementation. MMFF94 molecular dynamics (MD) simulation is used to study the stability of a 21-residue antimicrobial peptide named MSI-78, which is an amphipathic alpha-helical peptide designed as a synthetic analog to the Magainin family peptides. The MD simulation shows that the MSI-78 peptide exhibits random coil structure in aqueous solvent, but alpha-helical structure in the 2,2,2-trifluoroethanol/water (50:50 V/V) solvent. These results are in good agreement with experiments. The MD simulation also suggests that the preferential stabilization of the folded alpha-helical structure of MSI-78 in the 2,2,2-trifluoroethanol/water solvent is due to its lower dielectric constant as compared to aqueous solvent.
Advisor: Hui Li
Comments
A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science, Major: Chemistry, Under the Supervision of Professor Hui Li. Lincoln, Nebraska: May 2014
Copyright (c) 2014 Hongbo Zhu