ambertools

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

OFFICIAL: AnteChamber PYthon Parser interfacE

Python interface of cpptraj

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

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

Interface enabling use of ANI-style, and other NN-IPs in the Amber molecular dynamics software suite. Works with both Amber engines, sander and pmemd.

AMBER2LAMMPS: A Python Utility for Converting AMBER Molecular Dynamics Files to LAMMPS Data Format

Amber docker images for molecular dynamics

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

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

A QM-MM Tutorial of Enzyme Reaction Dynamics

🛠️ Create and manage AI agent identities with the Agent Commerce Protocol CLI for service trading and token launching on the Base chain.

This is an attempt to deposit the things I have learnt (and used) on how to do post-MD analysis on Amber. For more information, check out the Latest Ambertools manual in the link below

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.

Physics-based 3D structure prediction for long circular RNA. Secondary-structure consensus, segmented multi-predictor folding, coarse-grained REMD + metadynamics, all-atom reconstruction. Ships a 2,013 nt all-atom model and the checks to re-derive its numbers. Team JLU-FBH, iGEM 2026.

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

MLIP (Machine Learning Interatomic Potential) plugins for ML/MM MD simulations with AmberTools25.

An advanced course on molecular modeling focused on forcefields, molecular dynamics simulations using AmberTools and Gromacs and post molecular dynamics analysis and visualization

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