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Journal of Chemical Theory and Computation, ISSN 1549-9618, 12/2011, Volume 7, Issue 12, pp. 4026 - 4037
The Automated force field Topology Builder (ATB, http://compbio.biosci.uq.edu.au/atb) is a Web-accessible server that can provide topologies and parameters for... 
Molecular Mechanics | SYSTEM | SUITE | SOLVATION FREE-ENERGIES | MOLECULAR-DYNAMICS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | VALIDATION | CHEMISTRY, PHYSICAL | CRYSTALLOGRAPHY | PARAMETER SET | PROTEINS | HYDRATION | DERIVING ATOMIC CHARGES
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 08/2015, Volume 11, Issue 8, pp. 3829 - 3843
Journal Article
Journal Article
Journal of Computational Chemistry, ISSN 0192-8651, 01/2005, Volume 26, Issue 1, pp. 97 - 105
Journal Article
CHEMICAL REVIEWS, ISSN 0009-2665, 05/2016, Volume 116, Issue 9, pp. 5155 - 5187
Journal Article
International Journal of Quantum Chemistry, ISSN 0020-7608, 03/2011, Volume 111, Issue 3, pp. 711 - 721
In this work, we analyzed the influence of the charge model on the magnitudes of atomic charges and electrostatic energies for the binding of aromatic drug... 
atomic charges | DNA intercalators | electrostatic energy | ORGANIC-MOLECULES | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | NUCLEIC-ACIDS | DEPENDENCE | RESP MODEL | CONFORMATIONAL ENERGIES | MATHEMATICS, INTERDISCIPLINARY APPLICATIONS | FORCE-FIELD | BINDING | POISSON-BOLTZMANN EQUATION | DIPOLE-MOMENTS | DERIVING ATOMIC CHARGES
Journal Article
Computer Physics Communications, ISSN 0010-4655, 03/2016, Volume 200, pp. 190 - 198
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 04/2016, Volume 12, Issue 4, pp. 1824 - 1832
We show by tensor decomposition analyses that the molecular electrostatic potential for amino acid peptide models has an effective rank less than twice the... 
DENSITY | FIT | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | POTENTIALS | MODEL | CONFORMATIONAL DEPENDENCE | DERIVING ATOMIC CHARGES | MOMENTS | Errors | Peptides | Computation | Searching | Multipoles | Strategy | Mathematical models | Electrostatics
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 05/2007, Volume 3, Issue 3, pp. 1004 - 1013
We develop here a new method to fit the molecular electrostatic potentials obtained in quantum mechanical calculations to a set of classical electrostatic... 
DENSITY | WAVE-FUNCTIONS | ENERGY | IV CHARGE MODEL | HYDROCARBONS | POPULATION ANALYSIS | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | PARAMETERS | DISTRIBUTED MULTIPOLE ANALYSIS | INTERMOLECULAR INTERACTIONS | DERIVING ATOMIC CHARGES
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 01/2013, Volume 117, Issue 1, pp. 70 - 82
We studied the effect of using different heme group charge parametrization methods and schemes (Merz-Kollman, CHELPG, and single- and multiconformational RESP)... 
GROMOS FORCE-FIELD | ANGSTROM RESOLUTION | TETRAHAEM CYTOCHROME C | REDUCTION | CHEMISTRY, PHYSICAL | ENERGY TRANSDUCTION | REDOX | DESULFOVIBRIO-VULGARIS HILDENBOROUGH | BASIS-SET | DERIVING ATOMIC CHARGES
Journal Article
Bulletin of the Chemical Society of Japan, ISSN 0009-2673, 7/2017, Volume 90, Issue 7, pp. 831 - 837
Journal Article
JOURNAL OF PHYSICAL CHEMISTRY B, ISSN 1520-6106, 05/2019, Volume 123, Issue 19, pp. 4204 - 4219
Long MD simulations are carried out using a detailed all-atom force field to investigate the effect of pH or, equivalently, degree of ionization alpha(-) (= 0,... 
POLY(DIALLYLDIMETHYLAMMONIUM CHLORIDE) | PHASE-BEHAVIOR | POLYION COMPLEX VESICLES | AM1-BCC MODEL | CHEMISTRY, PHYSICAL | FORCE-FIELD | EFFICIENT GENERATION | POLYACRYLIC-ACID | HYALURONIC-ACID | DERIVING ATOMIC CHARGES | AQUEOUS-SOLUTION
Journal Article
The Journal of Physical Chemistry B, ISSN 1520-6106, 09/2017, Volume 121, Issue 35, pp. 8242 - 8262
Nitrogenase is the only enzyme that can break the triple bond in N2 to form two molecules of ammonia. The enzyme has been thoroughly studied with both... 
AUXILIARY BASIS-SETS | MOLECULAR-DYNAMICS | FEMO-COFACTOR | CENTRAL CARBON | FORCE-FIELD PARAMETERS | CHEMISTRY, PHYSICAL | DENSITY-FUNCTIONAL THEORY | ACIDITY CONSTANTS | DERIVING ATOMIC CHARGES | FREE-ENERGY SIMULATIONS | REORGANIZATION ENERGY | Naturvetenskap | Fysikalisk kemi | Natural Sciences | Kemi | Physical Chemistry | Chemical Sciences
Journal Article
Journal of Chemical Physics, ISSN 0021-9606, 01/2006, Volume 124, Issue 4, pp. 044703 - 044703-9
Potassium channels are membrane proteins known to select potassium over sodium ions at a high diffusion rate. We conducted ab initio calculations on a filter... 
STATES | FILTER | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | DYNAMICS | CHEMISTRY, PHYSICAL | CONDUCTION | KCSA CHANNEL | K+ CHANNEL | INSIGHT | BINDING | DERIVING ATOMIC CHARGES | PERMEATION | Potassium Channels - metabolism | Sodium - chemistry | Models, Biological | Computer Simulation | Models, Molecular | Ions | Potassium Channels - chemistry | Electric Conductivity | Kinetics | Potassium - chemistry
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 05/2011, Volume 7, Issue 5, pp. 1404 - 1414
Journal Article
Journal of Chemical Theory and Computation, ISSN 1549-9618, 06/2013, Volume 9, Issue 6, pp. 2718 - 2732
A set of geometrical parameters has been determined for single manganese metalloproteins for the AMBER force field, and ultimately to other force fields with a... 
DENSITY FUNCTIONALS | CYTOCHROME-C-OXIDASE | METAL-LIGAND INTERACTIONS | CRYSTAL-STRUCTURE | PHYSICS, ATOMIC, MOLECULAR & CHEMICAL | CHEMISTRY, PHYSICAL | POTENTIAL FUNCTIONS | CATALYTIC MECHANISM | FORCE-FIELD PARAMETERIZATION | SUPEROXIDE-DISMUTASE | MECHANICAL CALCULATIONS | DERIVING ATOMIC CHARGES
Journal Article
Computational and Theoretical Chemistry, ISSN 2210-271X, 08/2014, Volume 1042, pp. 1 - 7
[Display omitted] •The N atoms of PBO owned about twice negative ESP charge as that of O atoms.•The ESP charges of PBO are well consistent with the... 
Deformation electron density | Poly (p-phenylene benzobisoxazole) | Electrostatic potential | Charge distribution | ELECTRONIC POPULATION ANALYSIS | FT-RAMAN | CHEMISTRY, PHYSICAL | DENSITY | RIGID-ROD POLYMERS | ORBITAL METHODS | POLY(P-PHENYLENE BENZOBISOXAZOLE)