The DOI matches its Crossref record; 64 of the 64 references it cites were found in a registry or an index.
A fast and high-quality charge model for the next generation general AMBER force field
Open accessAbstract
The General AMBER Force Field (GAFF) has been broadly used by researchers all over the world to perform in silico simulations and modelings on diverse scientific topics, especially in the field of computer-aided drug design whose primary task is to accurately predict the affinity and selectivity of receptor–ligand binding. The atomic partial charges in GAFF and the second generation of GAFF (GAFF2) were originally developed with the quantum mechanics derived restrained electrostatic potential charge, but in practice, users usually adopt an efficient charge method, Austin Model 1-bond charge corrections (AM1-BCC), based on which, without expensive ab initio calculations, the atomic charges could be efficiently and conveniently obtained with the ANTECHAMBER module implemented in the AMBER software package. In this work, we developed a new set of BCC parameters specifically for GAFF2 using 442 neutral organic solutes covering diverse functional groups in aqueous solution. Compared to the original BCC parameter set, the new parameter set significantly reduced the mean unsigned error (MUE) of hydration free energies from 1.03 kcal/mol to 0.37 kcal/mol. More excitingly, this new AM1-BCC model also showed excellent performance in the solvation free energy (SFE) calculation on diverse solutes in various organic solvents across a range of different dielectric constants. In this large-scale test with totally 895 neutral organic solvent–solute systems, the new parameter set led to accurate SFE predictions with the MUE and the root-mean-square-error of 0.51 kcal/mol and 0.65 kcal/mol, respectively. This newly developed charge model, ABCG2, paved a promising path for the next generation GAFF development.
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Structural and thermodynamic framework for PIEZO1 modulation by small molecules
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Metadata
- Authors
- He, X., Man, V. H., Yang, W., Lee, T.-S., & Wang, J.
- Venue
- The Journal of Chemical Physics
- Publisher
- AIP Publishing
- Published
- 2020-09-16
- Volume
- 153
- Issue
- 11
- Pages
- 114502-114502
- ISSN
- 0021-9606 (ISSN-L)
- 1089-7690
- OpenAlex
- W3086801715
- Cited by
- 783
- References
- 64
- FWCI
- 18.75
- Type
- journal article
- Language
- en
- Open access
- green
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