STRC Research

gmx_MMPBSA

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gmx_MMPBSA

gmx_MMPBSA is the planned endpoint free-energy wrapper for h01 Phase 9b holo-MD + MM-PBSA / MM-GBSA rescoring.

Local install

  • Installed version: 1.6.4 via pip wheel (--no-deps) inside the conda env
  • Env: /opt/miniconda3/envs/strc-mmpbsa
  • Main executable: /opt/miniconda3/envs/strc-mmpbsa/bin/gmx_MMPBSA
  • Required runtime env: AMBERHOME=/opt/miniconda3/envs/strc-mmpbsa
  • Dependencies: Homebrew GROMACS, AmberTools 23.3, Python 3.10 stack

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
/opt/miniconda3/envs/strc-mmpbsa/bin/python -m pip install --no-deps gmx-mmpbsa==1.6.4
export AMBERHOME=/opt/miniconda3/envs/strc-mmpbsa
export PATH=$AMBERHOME/bin:/opt/homebrew/bin:$PATH

Note: conda-forge gmx_mmpbsa=1.6.3 was not installable with Python 3.11 because of old pandas constraints. The working local path is Python 3.10 + AmberTools 23.3 + pip wheel gmx-mmpbsa==1.6.4.

h01 use case

Phase 9b smoke: one v5.3 lead, WT vs E1659A, finite MM-PBSA / MM-GBSA numbers plus per-residue decomposition if the topology path is viable. The first run is a smoke test, not a production binding-free-energy proof.

Output formats

  • Text summaries: FINAL_RESULTS_MMPBSA.dat, FINAL_DECOMP_MMPBSA.dat
  • CSV-like intermediate tables from gmx_MMPBSA_ana
  • Amber-style topology files generated from GROMACS inputs

Risks

  • Requires compatible GROMACS topology and trajectory files; current h01 tauRAMD/OpenMM artifacts may need conversion or a separate OpenMM/AmberTools endpoint path.
  • 2026-04-27 h01 preflight: direct Phase 9b path is blocked because h01 has no native .top/.tpr/.xtc or Amber .prmtop/.inpcrd for matched WT/MUT v5.3 holo systems.
  • Endpoint energies are sensitive to dielectric choices and frame selection. Treat any first smoke as a tooling and sign check only.

License / source

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