Molecular Dynamics Simulations of Antimicrobial Peptide KU04AMP01 in complex with some conserved DNA-segments of Multi-Drug Resistant Pathogens

An experimental Antimicrobial Peptide, KU04AMP01, may eliminate Gram negative pathogens by damaging cellular barrier and genomic DNA. This repository contains codes and data of Molecular Dynamics of KU04AMP01 in complex with various segments of DNA taken that are common to the genomes of two pathogens, Acinetobacter baumannii and Pseudomonas aeruginosa. The conserved sequences were revealed computationally by analyzing the fastas of both bacterial genomes. This was followed by batch-docking of the DNA segments built from those sequences with a KU04AMP01 molecule using HDOCK, and subsequent molecular dynamics of the best-docked and worst-docked poses using GROMACS.