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Updated: Jun 24, 2026

Synthesizing Amino Acids Modified with Reactive Carbonyls in Silico to Assess Structural Effects Using Molecular Dynamics Simulations
Published on: April 26, 2024
The SAMP1 solvation challenge: further lessons regarding the pitfalls of parametrization
Anthony Nicholls1, Stanislaw Wlodek, J Andrew Grant
1OpenEye Scientific Software, Inc Santa Fe, New Mexico, USA. anthony@eyesopen.com
Abstract:
This paper describes an investigation into the performance of different charges and radii with the Poisson-Boltzmann method for the calculation of vacuum-water transfer energies. The test set consisted of 63 drug-like molecules used in a blind-test challenge. The results are consistent with earlier reports, namely, that more physical charges perform better and that radii parametrization can both improve and also dramatically worsen results, with the latter suggesting a failure to capture all of the basic physics of solvation.
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