Metadata-Version: 2.4
Name: ambertools-unofficial
Version: 26.0.0
Summary: AmberTools command-line programs packaged for pip
License-Expression: GPL-3.0-or-later AND LGPL-3.0-or-later AND BSD-3-Clause AND MIT
License-File: LICENSE
Requires-Python: >=3.10
Description-Content-Type: text/markdown

# ambertools-unofficial

**Unofficial** PyPI repackaging of [AmberTools](https://ambermd.org/AmberTools.php) 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, 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 26 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, 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.
