ambertools-unofficial 24.8.0.post1

AmberTools command-line programs packaged for pip

ambertools-unofficial

Unofficial PyPI repackaging of AmberTools command-line programs (antechamber, parmchk2, cpptraj, sander, tleap, and many more).

This package is not affiliated with or endorsed by the AmberTools developers at the University of California, San Francisco, Rutgers University, or any other contributing institution.

Installation

pip install ambertools-unofficial

The AMBERHOME environment variable is set automatically by wrapper scripts — no manual configuration needed.

Included compiled programs

antechamber, am1bcc, atomtype, bondtype, espgen, prepgen, respgen, match, match_atomname, parmchk2, parmcal, sqm, tleap / teLeap, cpptraj, ambpdb, sander, pbsa, simplepbsa, mdgx, reduce, paramfit, resp, nmode, gbnsr6, rism1d, rism3d.snglpnt, AddToBox, ChBox, PropPDB, UnitCell, mmpbsa_py_energy, mmpbsa_py_nabnmode, mm_pbsa_nabnmode, nfe-umbrella-slice, and more.

All compiled binaries are built with OpenMP support for multi-threaded execution. Thread count can be controlled with the OMP_NUM_THREADS environment variable.

Included Python scripts

The following pure-Python utilities from the AmberTools distribution are included and available as commands after installation:

• MMPBSA / ante-MMPBSA — MM-PBSA/MM-GBSA binding free energy analysis
• cpinutil / ceinutil / cpeinutil — constant pH/redox input preparation (requires pip install parmed)
• charmmlipid2amber — convert CHARMM lipid PDB files for use with Lipid14
• pyresp_gen / py_resp — Python RESP charge fitting
• fitpkaeo — pKa fitting (requires numpy, scipy)
• softcore_setup — prepare softcore TI input
• finddgref — free energy reference state finder
• genremdinputs — generate replica exchange MD inputs
• fixremdcouts — fix REMD output files
• remake_cpouts — deconvolute constant pH REMD cpout files

Not included

The following components from the full AmberTools distribution are not included in this package:

Component	Reason	Alternative
ParmEd	Python package with C extensions	pip install parmed
pytraj	Python/C++ bindings to cpptraj	pip install pytraj
pdb4amber	Standalone Python package	pip install pdb4amber
packmol_memgen	Complex bundled dependencies	Install via conda
mdout_analyzer	Requires tkinter GUI + matplotlib	Use parmed or manual parsing
bar_pbsa	Requires pytraj C extension	Install via conda
MPI variants (sander.MPI, etc.)	MPI requires system-specific libraries	Install via conda or build from source
CUDA variants	Requires NVIDIA GPU drivers	Install via conda or build from source
Python API (libsander, libpbsa bindings)	C extension modules	Install via conda

Source code

The binaries in this wheel are compiled from the official AmberTools 24 source code, which is freely available at:

https://ambermd.org/AmberTools.php

In accordance with the GNU General Public License v3 §6(d), the Corresponding Source for all GPL-licensed components can be obtained free of charge from the URL above.

License

AmberTools is distributed under a combination of licenses:

• GPL-3.0-or-later — the majority of AmberTools programs
• LGPL-3.0-or-later — libsander, libpbsa, libmdgx, BLEND (3D-RISM)
• BSD-3-Clause — arpack, ucpp, reduce, netcdf
• MIT — portions of ParmEd (fortranformat, chemistry.unit)
• CC-BY-SA-4.0 — DFTB parameter files (dat/slko)
• Public Domain — LAPACK, BLAS, force-field parameter files

See the LICENSE file distributed with this package for the full license texts.

This repackaging is provided under the same GPL-3.0-or-later terms.