Initial coordinates of 5 systems used for exploring the interactions between drug LIG1 and oncogenic KRAS4B G12D mutant while anchoring to cell membrane.
CHARMM36m FF parameter files of LIG1 and its isomer are reported here namely LIG1.prm, LIG1.rtf, LIG1-isomer.prm, and LIG1-isomer.rtf.
Python and Tcl scripts used for MD analysis and MD simulations were run using GROMACS.
A folder named "Binding-free-energy-calculation" is added for examples for biased force force calculations used in this project for calculating binding free-energy of LIG1 and its isomer with SII pocket of KRAS4B-G12D mutant on the PM.
The published paper can be found through this link: https://pubs.rsc.org/en/content/articlelanding/2023/nr/d3nr04513g