Paper Citing NAMD - Abstract
Perez, Alberto; MacCallum, Justin L.; Brini, Emiliano; Simmerling, Carlos; Dill, Ken A.
Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11:4770-4779, OCT 2015
Force fields, such as Amber's ff12SB, can be fairly accurate models of the physical forces in proteins and other biomolecules. When coupled with accurate solvation models, force fields are able to bring insight into the conformational preferences, transitions, pathways, and free energies for these biomolecules. When computational speed/cost matters, implicit solvent is often used but at the cost of accuracy. We present an empirical grid-like correction term, in the spirit of cMAPs, to the combination of the ff12SB protein force field and the GBneck2 implicit-solvent model. Ff12SB-cMAP is parametrized on experimental helicity data. We provide validation on a set of peptides and proteins. Ff12SB-cMAP successfully improves the secondary structure biases observed in ff12SB + Gbnecla. Ff12SB-cMAP can be downloaded (https://github.com/laufercenter/Arnap.git) and used within the Amber package. It can improve the agreement of force fields + implicit solvent with experiments.
