gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
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Oct 10, 2026 - Python
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ambertools
Here are 10 public repositories matching this topic...
OFFICIAL: AnteChamber PYthon Parser interfacE
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Oct 15, 2026 - Python
AMBER2LAMMPS: A Python Utility for Converting AMBER Molecular Dynamics Files to LAMMPS Data Format
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Mar 31, 2026 - Python
A collection of scripts written for use with different computational biology/chemistry packages throughout my PhD.
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May 9, 2024 - Python
xBFreE is a powerful and versatile tool for computing the Binding Free Energies using a variety of methods across popular Molecular Dynamics programs
charmm namd gromacs amber ambertools mmgbsa mmpbsa md-simulations energy-calculations gmx-mmpbsa gmx-mmgbsa
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Nov 14, 2023 - Python
MLIP (Machine Learning Interatomic Potential) plugins for ML/MM MD simulations with AmberTools25.
plugin molecular-dynamics-simulation orb mace ambertools md uma machine-learning-interatomic-potential mlip aimnet mlmm
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Oct 2, 2026 - Python
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.
structural-biology molecular-dynamics computational-biology pytorch openmm igem circrna ambertools coarse-grained rna-structure-prediction metadynamics viennarna replica-exchange igem-2026
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Oct 17, 2026 - Python
Python utility script to perform energy minimisation on a small molecule PDB file using AmberTools
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Apr 11, 2020 - Python
Automated QM/MM (GAMESS-US/MCPB.py), Boltzmann-weighted ensemble docking (GNINA 1.3), and 100 ns GPU Molecular Dynamics (OpenMM) pipeline via Snakemake to elucidate the allosteric rescue of human SIRT6 by MDL800.
snakemake molecular-dynamics openmm ambertools qmmm cadd computational-biophysics gnina allosteric-modulation sirt6
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Oct 19, 2026 - Python
Integrated workspace for preparing and inspecting all-atom protein–membrane molecular systems.
molecular-dynamics openmm computational-chemistry scientific-computing ambertools molecular-modeling membrane-proteins
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Oct 7, 2026 - Python
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