A Parameterization of the Generalized Born Model for Simulations with Only Torsional Degrees of Freedom
Robin Curtis, University of Manchester, PO Box 88, Sackville Street, Manchester, M 60 1QD, United Kingdom, James Magee, School of Chemical Engineering and Analytical Science, University of Manchester, PO Box 88, Sackville Street, Manchester M60 1QD, United Kingdom, and Michael W. Deem, Rice University, 6100 Main Street - MS 142, Houston, TX 77005-1892.
In all-atomistic simulations of peptides, the amount of phase space to be sampled can be reduced by constraining all but torsional degrees of freedom. Most forcefields have been developed for non-constrained systems, with a prominent exception being ECEPP. Polar solvation and screening effects are incorporated into ECEPP using solvent accessible surface area (SASA) models. A recent, more rigorous method to incorporate these effects is through use of Generalized Born (GB) models. In this work, a GB model is parameterized for the ECEPP forcefield by matching the electrostatic solvation free energy with that calculated from solving the Poisson equation for a trial set of energy-minimized amino acid structures. We compare results determined from simulations of homopolypeptides using the GB model with those determined using various SASA models and distance dependent dielectric. Further, different methods for incorporating salt effects into the GB model are investigated. Finally, we use Monte-Carlo simulations to determine the effect of salt concentration on the structures of self-assembling peptides such as poly-lysine and the octapeptide, AEAEAKAK.