biostudies-literatureCerutti DSNCRR NIH HHSNIGMS NIH HHS2328-38https://www.ebi.ac.uk/biostudies/studies/S-EPMC3622952biostudies-literatureUnknown117(8)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 transfThe journal of physical chemistry. BDerivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization.PMC3622952P41 RR006009GM-57513R01 GM057513Swope WCCerutti DSCase DARice JEfalseDerivation of fixed partial charges for amino acids accommodating a specific water model and implicit polarization.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 transf2013-01-01T00:00:00Z2013 Feb2025-04-04T20:29:38.944Z2019-03-27T01:07:16ZS-EPMC36229522337966410.1021/jp311851r