AmberTools

AmberTools provides MMPBSA.py, cpptraj, tleap, and topology utilities needed for h01 endpoint free-energy smoke tests.

Local install

• Installed version: AmberTools 23.3 from conda-forge
• Env: /opt/miniconda3/envs/strc-mmpbsa
• Executables present: MMPBSA.py, cpptraj, tleap, antechamber
• Required runtime env for MMPBSA.py: AMBERHOME=/opt/miniconda3/envs/strc-mmpbsa

Install command:

/opt/miniconda3/bin/conda create -y -n strc-mmpbsa -c conda-forge python=3.10 ambertools=23.3 pandas=1.5.3 numpy=1.26.4 scipy matplotlib-base seaborn tqdm h5py mpi4py

h01 use case

Fallback endpoint free-energy path if gmx_MMPBSA cannot consume existing h01 inputs directly. Also supplies ligand/receptor topology utilities for MM-PBSA smoke setup.

2026-04-27 h01 preflight: AmberTools itself is callable, but post-hoc OpenMM XML → Amber topology conversion of the Phase 5q E1659A holo system is blocked because ParmEd finds 37,405 bonds without Amber bond types. Build matched WT/MUT Amber-compatible systems directly for Phase 9b instead.

Output formats

• Amber topology: .prmtop, .inpcrd
• Trajectory analysis: .nc, .mdcrd, .dat
• MMPBSA outputs: FINAL_RESULTS_MMPBSA.dat, decomposition tables

Apple Silicon note

This is CPU tooling. Use it for setup, topology conversion, and short endpoint analysis. Do not launch multi-hour CPU-only MD without an explicit runtime decision.

License / source

• License: AmberTools open-source license
• Source: https://ambermd.org/AmberTools.php

Connections

• [applies] STRC h01 Phase 9b Holo MD MM-PBSA 2026-04-27 SKELETON
• [see-also] gmx_MMPBSA
• [see-also] GROMACS
• [part-of] STRC Tools
• [part-of] Tools index