This repository contains the four starting structures of KE15-DNA complex stated in paper J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.2c00765. The input file of both the reactant state and transition state for molecular dynamic simulations are also provided, along with parameter file used.
The present folder contains the following files:
KE15_DNAi where i ranges from 1 to 4 are the starting structures (in PDB format) of the four KE15-DNA complexes as described in the paper.
KE15_DNAi_j_RS where i ranges from 1 to 4 and j from 1 to 25 are the MD input files (in Tinker XYZ and PDB format) of the solvated KE15-DNA complexes in the reactant state, as described in the paper.
KE15_DNAi_j_TS where i ranges from 1 to 4 and j from 1 to 25 are the MD input files (in Tinker XYZ and PDB format) of the solvated KE15-DNA complexes in the transition state, as described in the paper.
amoebabio18_ligRS.prm and amoebabio18_ligTS.prm are the AMOEBA parameter files corresponding to the above structures.