1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations

Abstract

The quality of the 1.14*CM1A and 1.20*CM5 charge models was evaluated for calculations of free energies of hydration. For a set of 426 neutral molecules, 1.14*CM1A and 1.20*CM5 yield MADs of 1.26 and 1.20 kcal/mol, respectively. The 1.14*CM1A charges, which can be readily obtained for large systems, exhibit large deviations only for a subset of functional groups. The results for these cases were systematically improved using Localized Bond Charge Corrections (LBCC) by which off-setting adjustments are made to the partial charges for atoms in specified bond types. Only 19 LBCCs were needed to yield 1.14*CM1A-LBCC charges that reduce the errors for the 426 ΔGhyd values to only 0.61 kcal/mol. The modified charge method was also tested in computation of heats of vaporization and densities for pure organic liquids, yielding average errors of 1.40 kcal/mol and 0.024 g/cm3, similar to those for 1.14*CM1A.

Comprehensive Evaluation of the Efficiency of Yeast Cell Wall Extract to Adsorb Ochratoxin A and Mitigate Accumulation of the Toxin in Broiler Chickens

“…Molecular dynamics were investigated using several open-source programs: (1) doGlycans (v1.0, Open Source program under GNU General Public License, v3.0, Free Software Foundation Inc, Boston, MA, USA), a tool to prepare carbohydrate structures under an Optimized Potentials for Liquid Simulations for All Atoms (OPLS-AA) modified force-field and related topology files for simulation [39] was used under Python 3 script and the Conda management system (Anaconda Inc., Austin, TX, USA) applied to the β-d-glucans receptor; (2) TopolGen (v1.1, Open Source Program under GNU General Public License, v3.0, Free Software Foundation Inc., Boston, MA, USA), a Perl script, and LigParGen (Open Source Program,http://zarbi.chem.yale.edu/ligpargen/) were used to produced GROMACS-formatted topology from the above generated PDB files docking experiment, compatible with an OPLS-AA force-field for OTA [40][41][42]; (3) GROMACS 2019.1 (GROMACS, Open Source Program under GNU General Public License, v3.0, Free Software Foundation Inc., Boston, MA, USA, www.gromacs.org, [43]) molecular dynamics simulation package was used to simulate receptor-ligand complex over 10 ns in a neutralized solvated system (water) at 37 • C and to study the initiation of the interaction energy at different charge states corresponding to a pH simulation performed at pH 3.0 and 6.5 to match our in vitro evaluations [44,45]. OTA was restrained using a force constant of 1000 kJ mol −1 nm −2 while the constrained and unconstrained structure of β-d-glucans were evaluated.…”

Solvation free energiesviaalchemical simulations: let's get honest about sampling, once more

“…61 The BAR estimates for the solva-tion energy of SM02 in water and 1-octanol using the GAFF2 force field are found to be ∆G(w) = −5.52 ± 0.14 kcal mol −1 and ∆G(o) = −15.10 ± 0.15 kcal mol −1 , respectively, yielding a partition coefficient of LogP = 7.05 ± 0.21. NEW computations using the OPLS-AA force field 6,62 (work data not shown) yields LogP = 6.24 ± 0.43. The experimental LogP value for SM02 is 4.1 Full SAMPL6 data are availble in Ref.…”

“…Solvation free energies and binding free energies of drug size molecules can nowadays be computed using seemingly well established computational techniques based on Free Energy Perturbation method (FEP) 3 with the system being represented by accurate atomistic force fields. [4][5][6] In FEP, the free energy between two end states, say 1 (gas-phase solute) and 0 (solvated solute), is given by e −β ∆G = e −β ∆U 0 (1) where ∆U = U 1 − U 0 is the potential energy difference between a Department of Chemistry, University of Florence, Italy. E-mail: procacci@unifi.it † Electronic Supplementary Information (ESI) available: MBAR computed 2D FES as a function of the θ , φ dihedral angles.…”

MembrFactory: A Force Field and composition Double Independent Universal Tool for Constructing Polyamide Reverse Osmosis Membranes

“…Since MembrFactory is independent of the force field, the topology files of the monomers can be obtained by a variety of tools. Examples of such tools are the Antechamber for the AMBER force field, the LigParGen web servers for the OPLS force field and the ParamChem web server for the CHARMM force field. The new atom types created after the bonding reaction between monomers' functional groups should be added manually in the topology file (details in the Supporting Information).…”

“…Here, we evaluated the performance of several popular force fields in MembrFactory, including AMBER, OPLS, and CHARMM. Antechamber, LigParGen web servers and Force Field Toolkit (ffTK) are used to generate parameter files for these force fields, respectively. The PA RO membrane model is formed from TMC and MPD, since these two monomers have been successfully and widely used in the preparation of RO membranes.…”