Python utility script to perform energy minimisation on a small molecule PDB file using AmberTools

A collection of scripts written for use with different computational biology/chemistry packages throughout my PhD.

AM1 specific reaction parameters for DHFR catalyzed reaction in sqm (AmberTools18)

Guide for Molecular dynamics (MD) simulations with AMBER Software on ASU Sol cluster

This my personal website

Collections of files and tools for weighted ensemble simulations of full-length APOBEC3B

When calculating the protein-ligand complex system, it is necessary to add an appropriate force field to the ligand. One effective method is to use the CGenFF service, but it was found that this function does not support the alkyne/alkene structure, so a script was written to use GAFF to process small molecules.

xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs

Repository for AmberTools Mission framework type in Galileo.

Amber docker images for molecular dynamics

Exploring the conformational ensembles of protein-protein complexes with transformer-based generative neural networks

Python interface of cpptraj

OFFICIAL: AnteChamber PYthon Parser interfacE

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.