ambertools 开源项目推荐（29 个）

Valdes-Tresanco-MS /gmx_MMPBSA

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

alanwilter /acpype

OFFICIAL: AnteChamber PYthon Parser interfacE

Amber-MD /pytraj

Python interface of cpptraj

John-Kazan /MDGuide

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

AspirinCode /AlphaPPImd

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

roitberg-group /torchani-amber

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.

askforarun /AMBER2LAMMPS

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

yylonly /AmberDocker

Amber docker images for molecular dynamics

crfield18 /PhD-scripts

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

xBFreEnergy /xBFreE

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

KhangLuong314 /ActiveSite-QM-MM

Autonomous multi-agent system for QM/MM computational chemistry simulation that designs, executes, and explains its scientific decisions. Built for Open Agent Hackathon 2026 (Track 02).

hopanoid /Enzyme-Reaction-Dynamics-Tutorial

A QM-MM Tutorial of Enzyme Reaction Dynamics

hit7z /openclaw-acp

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

kol0760 /AMBER_calculate_for_gromacs

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.

SHEDOOMTC /AmberTools-Analysis-Quick

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

RomanCohort /Torusfold-physics

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.

t-0hmura /amber-mlips

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

aretasg /amber-emm

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

xBFreEnergy /xBFreEnergy.github.io

该项目在 GitHub 上没有填写描述

suleymanselim /AmberTutorials

该项目在 GitHub 上没有填写描述