Abstract
We have developed the IPolQ method for fitting nonpolarizable point charges to implicitly represent the energy of polarization for systems in pure water. The method involves iterative cycles of molecular dynamics simulations to estimate the water charge density around the solute of interest, followed by quantum mechanical calculations at the MP2/cc-pV(T+d)Z level to determine updated solute charges. Lennard-Jones parameters are updated starting from the Amber FF99SB nonbonded parameter set to accommodate the new charge model, guided by the comparisons to experimental hydration free energies (HFEs) of neutral amino acid side chain analogs and assumptions about the computed HFEs for charged side chains. These Lennard-Jones parameter adjustments for side-chain analogs are assumed to be transferable to amino acids generally, and new charges for all standard amino acids are then derived in the presence of water modeled by TIP4P-Ew. Overall, the new charges depict substantially more polarized amino acids, particularly in the backbone moieties, than previous Amber charge sets. Efforts to complete a new force field with appropriate torsion parameters for this charge model are underway. The IPolQ method is general and applicable to arbitrary solutes.
Keywords
Partial chargeWater modelSide chainForce field (fiction)ChemistryCharge (physics)Point particleMolecular dynamicsAmino acidComputational chemistryPolarization (electrochemistry)Torsion (gastropod)Statistical physicsAtomic chargeThermodynamicsPhysicsChemical physicsMoleculeClassical mechanicsPhysical chemistryQuantum mechanicsOrganic chemistry
Affiliated Institutions
Related Publications
Improved side‐chain torsion potentials for the Amber ff99SB protein force field
Abstract Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accurac...
Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator
A procedure to determine the electrostatic parameters has been developed for a polarizable empirical force field based on the classical Drude oscillator model. Atomic charges an...
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB
Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structur...
Effects of Charge Localization on the Orbital Energies of Bithiophene Clusters
Standard and constrained density functional theory calculations were used to study the degree of charge localization in positively charged bithiophene clusters. Although polariz...
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
Abstract A first‐generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic har...
Publication Info
- Year
- 2013
- Type
- article
- Volume
- 117
- Issue
- 8
- Pages
- 2328-2338
- Citations
- 115
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
115
OpenAlex
Cite This
David S. Cerutti,
Julia E. Rice,
William C. Swope
et al.
(2013).
Derivation of Fixed Partial Charges for Amino Acids Accommodating a Specific Water Model and Implicit Polarization.
The Journal of Physical Chemistry B
, 117
(8)
, 2328-2338.
https://doi.org/10.1021/jp311851r
Identifiers
- DOI
- 10.1021/jp311851r