Journal
CHEMPHYSCHEM
Volume 16, Issue 8, Pages 1739-1749Publisher
WILEY-V C H VERLAG GMBH
DOI: 10.1002/cphc.201402861
Keywords
continuum electrostatics; molecular dynamics; reaction field; solvation free energy; solvent effects
Funding
- Deutsche Forschungsgemeinschaft [SFB749]
- CIPSM
Ask authors/readers for more resources
Optimization of the Hamiltonian dielectric solvent (HADES) method for biomolecular simulations in a dielectric continuum is presented with the goal of calculating accurate absolute solvation free energies while retaining the model's accuracy in predicting conformational free-energy differences. The solvation free energies of neutral and polar amino acid side-chain analogs calculated by using HADES, which may optionally include nonpolar contributions, were optimized against experimental data to reach a chemical accuracy of about 0.5 kcalmol(-1). The new parameters were evaluated for charged side-chain analogs. The HADES results were compared with explicit-solvent, generalized Born, Poisson-Boltzmann, and QM-based methods. The potentials of mean force (PMFs) between pairs of side-chain analogs obtained by using HADES and explicit-solvent simulations were used to evaluate the effects of the improved parameters optimized for solvation free energies on intermolecular potentials.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available