Driving torsion scans with wavefront propagation

Qiu, Yudong; Smith, Daniel G. A.; Stern, Chaya; Feng, Mudong; Jang, Hyesu; Wang, Lee‐Ping

doi:10.1063/5.0009232

Cited by 37 publications

(46 citation statements)

References 54 publications

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“…54 The single-point energies and gradients were computed for constrained energyminimized structures where constraints were varied over 2-D grids of main-chain or side-chain dihedral angles. The TorsionDrive 67 procedure was employed to generate the grids of constrained optimized structures using a wavefront propagation method, as illustrated in Figure 1. The procedure starts with a user-specified grid of dihedral angle constraints and one or more initial structures.…”

Section: ■ Methodsmentioning

confidence: 99%

Development and Validation of AMBER-FB15-Compatible Force Field Parameters for Phosphorylated Amino Acids

Stoppelman

Nerenberg

et al. 2021

J. Phys. Chem. B

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Phosphorylation of select amino acid residues is one of the most common biological mechanisms for regulating protein structures and functions. While computational modeling can be used to explore the detailed structural changes associated with phosphorylation, most molecular mechanics force fields developed for the simulation of phosphoproteins have been noted to be inconsistent with experimental data. In this work, we parameterize force fields for the phosphorylated forms of the amino acids serine, threonine, and tyrosine using the ForceBalance software package with the goal of improving agreement with experiments for these residues. Our optimized force field, denoted as FB18, is parameterized using high-quality ab initio potential energy scans and is designed to be fully compatible with the AMBER-FB15 protein force field. When utilized in MD simulations together with the TIP3P-FB water model, we find that FB18 consistently enhances the prediction of experimental quantities such as 3 J NMR couplings and intramolecular hydrogen-bonding propensities in comparison to previously published models. As was reported with AMBER-FB15, we also see improved agreement with the reference QM calculations in regions at and away from local minima. We thus believe that the FB18 parameter set provides a promising route for the further investigation of the varied effects of protein phosphorylation.

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Section: ■ Methodsmentioning

confidence: 99%

Development and Validation of AMBER-FB15-Compatible Force Field Parameters for Phosphorylated Amino Acids

Stoppelman

Nerenberg

et al. 2021

J. Phys. Chem. B

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“…Quantum mechanical energy profiles were generated for dihedral angles in the Roche and Coverage sets (see, for example, Figure ). All calculations were carried out on the MQCAS, which employs TorsionDrive software to compute each torsion energy profile using a wavefront propagation procedure, described briefly here. Multiple initial geometries were generated for each molecule via Fragmenter and provided as input at the start of the procedure.…”

Section: Methodsmentioning

confidence: 99%

Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field

Qiu

Smith

Boothroyd

et al. 2021

J. Chem. Theory Comput.

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113

162

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We present a methodology for defining and optimizing a general force field for classical molecular simulations, and we describe its use to derive the Open Force Field 1.0.0 smallmolecule force field, codenamed Parsley. Rather than using traditional atom typing, our approach is built on the SMIRKSnative Open Force Field (SMIRNOFF) parameter assignment formalism, which handles increases in the diversity and specificity of the force field definition without needlessly increasing the complexity of the specification. Parameters are optimized with the ForceBalance tool, based on reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These quantum reference data are computed and are maintained with QCArchive, an opensource and freely available distributed computing and database software ecosystem. In this initial application of the method, we present essentially a full optimization of all valence parameters and report tests of the resulting force field against compounds and data types outside the training set. These tests show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields, as is accuracy on binding free energies. We find that this initial Parsley force field affords accuracy similar to that of other general force fields when used to calculate relative binding free energies spanning 199 protein−ligand systems. Additionally, the resulting infrastructure allows us to rapidly optimize an entirely new force field with minimal human intervention.

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“…All calculations were carried out on the MQCAS, which employs the TorsionDrive software to compute each torsion energy profile using a wavefront propagation procedure, [56] For compounds in the Roche Set, torsional scans were generated for the 819 dihedral angles matching all of the following conditions:…”

Section: Vibrational Frequenciesmentioning

confidence: 99%

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

Qiu¹,

Smith²,

Boothroyd³

et al. 2020

Preprint

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We describe the structure and optimization of the Open Force Field 1.0.0 small molecule force field, code-named Parsley. Parsley uses the SMIRKS-native Open Force Field (SMIRNOFF) parameter assignment formalism in which parameter types are assigned directly by chemical perception, in contrast to traditional atom type-based approaches. This method provides a natural means to incorporate increasingly diverse chemistry without needlessly increasing force field complexity. In this work, we present essentially a full optimization of the valence parameters in the force field. The optimization was carried out with the ForceBalance tool and was informed by reference quantum chemical data that include torsion potential energy profiles, optimized gas-phase structures, and vibrational frequencies. These data were computed and are maintained with QCArchive, an open-source and freely available distributed computing and database software ecosystem. Tests of the resulting force field against compounds and data types outside the training set show improvements in optimized geometries and conformational energetics and demonstrate that Parsley's accuracy for liquid properties is similar to that of other general force fields. <br>

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Driving torsion scans with wavefront propagation

Cited by 37 publications

References 54 publications

Development and Validation of AMBER-FB15-Compatible Force Field Parameters for Phosphorylated Amino Acids

Development and Validation of AMBER-FB15-Compatible Force Field Parameters for Phosphorylated Amino Acids

Development and Benchmarking of Open Force Field v1.0.0—the Parsley Small-Molecule Force Field

Development and Benchmarking of Open Force Field v1.0.0, the Parsley Small Molecule Force Field

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