Comparison of semi-empirical quantum mechanics methods applied to biological molecules: Potential and free energy surfaces of alanine and glycine Dipeptides in vacuum and in water

COMP 333

Gustavo de M. Seabra, seabra@qtp.ufl.edu, Quantum Theory Project, University of Florida, 2300 New Physics Building, PO Box 118435, Gainesville, FL 32611-8435, Ross C Walker, rcw@sdsc.edu, Strategic Applications Computing, San Diego Supercomputing Center, University of California, San Diego, 9500 Gilman Drive #0505, La Jolla, CA 92093, and Adrian E Roitberg, Department of Chemistry, University of Florida, Quantum Theory Project, Gainesville, FL 32611.
The Amber 9 version of the molecular dynamics package contains a native implementation of an array of semi-empirical methods. Included are MNDO, AM1, PM3, PDDG/MNDO, PDDG/PM3, PM3CARB1 and SCC-DFTB.

We show calculations of the adiabatic potential energy surface for alanine and glycine dipeptides in vacuum and using AM1, PM3, PDDG/PM3 and SCC-DFTB semi-empirical methods for the dipeptide, and compare it to high level ab-initio data obtained using Gaussian 03.

Results for the free energy surfaces of alanine and glycine dipeptides in water calculated from a 30 ns molecular dynamics run for each of the semi-empirical methods above, and using both TIP3P and TIP4Pew models for water, will also be presented.

 

Poster Session
6:00 PM-8:00 PM, Tuesday, August 21, 2007 BCEC -- Ballroom Foyer, Poster

Sci-Mix
8:00 PM-10:00 PM, Monday, August 20, 2007 BCEC -- Exhibit Hall - B2, Sci-Mix

Division of Computers in Chemistry

The 234th ACS National Meeting, Boston, MA, August 19-23, 2007