Valence state parameters of all transition metal atoms in metalloproteins-development of ABEEMσπ fluctuating charge force field

A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons

(2014) Oliwia M. Szklarczyk et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

(2014) Fernanda Duarte et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Studies on the Structural Properties of NAMI-A in Aqueous Solution by Combined QM and ABEEM/MM Method

(2013) Huiyuan Zou et al.   ACTA CHIMICA SINICA

A Polarizable Force-Field for Cholesterol and Sphingomyelin

(2013) David Robinson   Journal of Chemical Theory and Computation

Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins

(2013) Rui P. P. Neves et al.   Journal of Chemical Theory and Computation

Matching of Additive and Polarizable Force Fields for Multiscale Condensed Phase Simulations

(2013) Christopher M. Baker et al.   Journal of Chemical Theory and Computation

Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator

(2013) Pedro E. M. Lopes et al.   Journal of Chemical Theory and Computation

Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field

(2013) Cui Liu et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

All-Atom Force Field for Molecular Dynamics Simulations on Organotransition Metal Solids and Liquids. Application to M(CO)n (M = Cr, Fe, Ni, Mo, Ru, or W) Compounds

(2013) Carlos E. S. Bernardes et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Partial Atomic Charges and Screened Charge Models of the Electrostatic Potential

(2012) Bo Wang et al.   Journal of Chemical Theory and Computation

Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential

(2012) Jiajing Zhang et al.   Journal of Chemical Theory and Computation

Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed Phases

(2012) Aleksandr V. Marenich et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

Development of Polarizable Models for Molecular Mechanical Calculations. 4. van der Waals Parametrization

(2012) Junmei Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Development and applications of the ABEEM fluctuating charge molecular force field in the ion-containing systems

(2012) LiDong Gong   Science China-Chemistry

Cation−π and π–π Interactions in Aqueous Solution Studied Using Polarizable Potential Models

(2011) Esam A. Orabi et al.   Journal of Chemical Theory and Computation

Evaluation of DNA Force Fields in Implicit Solvation

(2011) Thomas Gaillard et al.   Journal of Chemical Theory and Computation

Polarizable Atomic Multipole-Based Molecular Mechanics for Organic Molecules

(2011) Pengyu Ren et al.   Journal of Chemical Theory and Computation

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

(2011) LiHong Hu et al.   Journal of Chemical Theory and Computation

Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium

(2011) Katarina Hart et al.   Journal of Chemical Theory and Computation

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Assessment of Atomic Charge Models for Gas-Phase Computations on Polypeptides

(2011) Toon Verstraelen et al.   Journal of Chemical Theory and Computation

Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system

(2011) Cui Liu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA

(2011) Elizabeth J. Denning et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Systemic Investigation of Hydrogen Peroxide Clusters (H2O2)n(n= 1−6) and Liquid-State Hydrogen Peroxide: Based on Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics and Molecular Dynamics

(2011) Chun-Yang Yu et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Recent developments and applications of the CHARMM force fields

(2011) Xiao Zhu et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Calculations of the Free Energy of Interaction of the c-Fos−c-Jun Coiled Coil: Effects of the Solvation Model and the Inclusion of Polarization Effects

(2010) Zhili Zuo et al.   Journal of Chemical Information and Modeling

Study on structures and properties of ammonia clusters (NH3)n (n=1–5) and liquid ammonia in terms of ab initio method and atom-bond electronegativity equalization method ammonia-8P fluctuating charge potential model

(2010) Ling Yu et al.   JOURNAL OF CHEMICAL PHYSICS

Development of a Polarizable Force Field Using Multiple Fluctuating Charges per Atom

(2010) Dong-Xia Zhao et al.   Journal of Chemical Theory and Computation

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

(2010) Christopher M. Baker et al.   Journal of Chemical Theory and Computation

Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF)

(2010) Martin B. Peters et al.   Journal of Chemical Theory and Computation

Including Charge Penetration Effects in Molecular Modeling

(2010) Bo Wang et al.   Journal of Chemical Theory and Computation

Current Status of the AMOEBA Polarizable Force Field

(2010) Jay W. Ponder et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model

(2010) Christopher M. Baker et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers

(2009) Christopher M. Baker et al.   JOURNAL OF MOLECULAR MODELING

Studies on the torsions of nucleic acids using ABEEMσπ/MM method

(2009) Fang-Fang Wang et al.   JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM

Ab initio and ABEEM/MM fluctuating charge model studies of dimethyl phosphate anion in a microhydrated environment

(2009) Fang-Fang Wang et al.   THEORETICAL CHEMISTRY ACCOUNTS

Do the Local Softness and Hardness Indicate the Softest and Hardest Regions of a Molecule?

(2008) Miquel Torrent-Sucarrat et al.   CHEMISTRY-A EUROPEAN JOURNAL

Application of a polarizable force field to calculations of relative protein-ligand binding affinities

(2008) O. Khoruzhii et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An intramolecular induction correction model of the molecular dipole moment

(2007) Asbjørn Holt et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY