Data for the manuscript entitled "Substrate binding and channeling allosterically modulate the interactions within the AlkB-AlkG electron transfer complex"

This repository provides CHARMM-compatible topology (top) and parameter (par) plain-text files (UTF-8) for molecular dynamics simulations of the FtAlkBG monooxygenase. Files can be opened in any text editor and are directly usable with NAMD (free for academic use) and CHARMM.Contents: Definitions of atom types and partial charges; bonded terms (bonds, angles, dihedrals, impropers); and nonbonded parameters for two metal sites:Site3 (AlkG): Fe coordinated by four cysteines — top_all27_Site3.inp, par_all27_Site3.inp.Site1/2 (AlkB): di-iron site coordinated by nine histidines and one glutamate — top_all27_Site1_2.inp, par_all27_Site1_2.inp.Project context: This dataset supports molecular dynamics studies of the FtAlkBG monooxygenase, which operates through two coordinated catalytic metal centers: a di-iron site in the AlkB domain (here split into Site1 and Site2 in the topology) and an Fe–(Cys)_4 site in the AlkG domain (Site3). The provided TOP/PAR files supply the necessary atom types, partial charges, and bonded/nonbonded parameters to model these centers and their coordination environments. They are intended for integration into NAMD/CHARMM simulations of FtAlkBG and related constructs.Force field & units: CHARMM27; energies in kcal/mol, distances in Å, angles in degrees.Software used: NAMD v2.14Data authors:Karolina Mikulska-Ruminska - created the files Mehmed Zahid Ertem - provided partial charges and geometry via QM/MM calculationsFunding: Physical Biosciences Program within the US Department of Energy (DOE), Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences (grant no KC030402); computational resources at the Center for Functional Nanomaterials, which is a U.S. Department of Energy Office of Science Facility, and the Scientific Data and Computing Center, a component of the Computational Science Initiative, at Brookhaven National Laboratory under Contract No. DE-SC0012704, by National Institutes of Health grants R01 GM139297 and R01 DK116780; Polish National Science Centre no. 2022/46/E/ST4/00053.See README.md for file organization and usage instructions.