packmol-memgen-minimal 1.1.20

A fork of packmol_memgen from AmberTools, a PACKMOL wrapper for packing proteins into membranes, aimed to be minimal, mordernized and self-contained.

PACKMOL MEMGEN MINIMAL 2026.1.8

Xiaoxuan Yu 2026-01-08

THIS FORK NOTES

This repository is a fork of packmol-memgen. The original README content is preserved below; this section summarizes the changes and current behavior.

• Packaging: this fork is published on PyPI (sdist/wheel). The Python wheel aims to avoid system-level dependencies (e.g., no AmberTools requirement). Some features include SIRAH coarse-graining support, minimization, parametrization and protonation using reduce are not available in this fork.

• Packmol: packing is performed by the external PACKMOL command-line tool. This package does not bundle PACKMOL; it is expected to be available on PATH. For convenience, it can be installed via an optional dependency (extra).

• Membrane orientation: membrane alignment/orientation is performed via MemPrO (Python + JAX) instead of the upstream memembed/ppm3 workflow. MemPrO is invoked via subprocess as an external command-line tool. MemPrO is not bundled into this package but can be installed via an optional dependency for convenience.

• Protonation: protonation uses pdb2pqr when needed.

• Output location: use --outdir DIR to write all generated files (final --output, --log, --packlog scripts/logs, intermediate structures) into a single directory.

Martini Auto-Mapping (MemPrO/Insane4MemPrO)

When --martini is enabled, the script can auto-build --insane_args for MemPrO/Insane4MemPrO with the following behavior:

• Lipids: --lipids + --ratio map to Insane -l/-u. // syntax is supported for lower/upper leaflets. Two --lipids entries are supported and map to Insane -l/-u (inner membrane) and -lo/-uo (outer membrane).

• Box size: --dims is converted from Angstrom to nm and passed as -x/-y/-z.

• Curvature: --curvature or --curv_radius maps to -curv c0,0,dir where c0 = abs(curvature), dir = sign(curvature).

• Solvents: --solvents + --solvent_ratio map to -sol entries. The only automatic name mapping is WAT -> W, which emits a warning once. All other solvent names must match Insane solventParticles (see packmol_memgen/data/insane_solvents.txt).

• Salts: --salt, --salt_c, --salt_a map to -posi_c0/1/2 and -negi_c0/1/2 using ion tokens stripped to letters (e.g. Na+ -> NA). --saltcon maps to -ion_conc with the value replicated for all three compartments.

The following options are not supported in Martini auto-mapping and will emit warnings: --distxy_fix, --dist, --dist_wat, --xygauss, --apl_offset, --lip_offset, --pbc, --nocounter, --charge_imbalance, --imbalance_ion. You can still supply custom --insane_args to override or extend the auto-generated arguments.

Installation

Minimal installation (this fork without PACKMOL or MemPrO):

pip install packmol-memgen-minimal

With optional packmol as a dependency:

pip install packmol-memgen-minimal[packmol]

With optional mempro as a dependency:

pip install packmol-memgen-minimal[mempro]

With both optional dependencies:

pip install packmol-memgen-minimal[full]

You may prefer mordern Python packaging tools such as uv to install

uv tool install packmol-memgen-minimal

extras are supported in uv as well. Other tools may work similarly.

LICENSE NOTE

This fork is distributed under GPL-2.0-only, inherited from the upstream project.

MemPrO is an optional external command-line tool distributed under the GNU GPL v3. This project interacts with MemPrO via subprocess calls; MemPrO is not bundled into this package and its license applies to MemPrO itself.

The martini force field parameter file packmol_memgen/data/martini_v3.0.0.itp is sourced from https://github.com/Martini-Force-Field-Initiative/martini-forcefields and is distributed under the Apache License 2.0. The full Apache 2.0 license text is provided at packmol_memgen/data/LICENSE.Apache-2.0.

CREDITS

This project depends on and/or interoperates with the following open-source software. Please refer to each project for license terms.

Core dependencies (installed via PyPI):

• NumPy (https://github.com/numpy/numpy)

• SciPy (https://github.com/scipy/scipy)

• pandas (https://github.com/pandas-dev/pandas)

• tqdm (https://github.com/tqdm/tqdm)

• matplotlib (https://github.com/matplotlib/matplotlib)

• PDB2PQR (https://github.com/Electrostatics/pdb2pqr)

• docopt (https://github.com/docopt/docopt)

Optional external tools (installed separately; invoked via subprocess):

• PACKMOL (MIT License, https://github.com/m3g/packmol)

• MemPrO (GNU GPL v3, https://github.com/ShufflerBardOnTheEdge/MemPrO)

Additional utilities used by this workflow:

• PDBREMIX (MIT License, https://github.com/boscoh/pdbremix)

• charmmlipid2amber (GPL-2.0, from AmberTools 2025, https://ambermd.org/AmberTools.php)

• Martini 3 force field parameters (Apache-2.0, https://github.com/Martini-Force-Field-Initiative/martini-forcefields)

PACKMOL MEMGEN 2023.8.8

Stephan N. Schott V. 2016-11-07

INSTALLATION

The main installation of Packmol Memgen is intended to be installed within AmberTools20. If that is not the case the following instructions could be follow to make it run as a stand-alone, though it is not officially supported.

Dependencies: Boost (tested with 1.54 or above) gfortran & gcc (tested with 4.8 and above) python 2.7 (or above)

The script should work as is. Includes a setup.py script which should work as usual:

python setup.py install

or

pip install .

You can specify a custom installation location with –home=<FOLDER> or –prefix=<FOLDER>, respectively. Testing of the software can be performed in the example folder, by executing “./example.sh”. This folder can be easily cleaned by executing “./example.sh clean”

CHANGELOG

2025.3.22

• Added initial functionality to support Packmol’s PBC option

2025.3.17

• Added onlyleapin flag to generate a template leap input without parametrizing.

• Modified memembed with Claude 3.7 suggestions to stop using boost.

• Updated packmol to 20.16

2025.2.10

• Force using propka for titration with_ph in pdb2pqr

2025.1.29

• Bugfix calculating center of PDB. This could have caused issues in calculating volumes, mainly in solvated systems.

2024.3.27

• Changed MEMEMBED to push TER to output file

2024.3.18:

• Separation of function in classes

• Better management of ppm3 alignment function

2024.2.9:

• Fixed help typo

• PACKMOL Update to fix FORCED output

2023.8.8:

• Added siWT4 COM to avoid overlaps

• Fixed deprecated np.float calls

• Added ppm3 support and code

• Shift water box if –dims is used to add at least 5A water on membrane surface

• Add packmol finetuning parameters

2023.2.24:

• Changed versioning to CalVer

• Updated packmol

• Added all amber supported ions and OPC3

• Added option to generate HMR systems

• Added control for minimization function and pmemd.cuda

• Added option to use pdb2pqr to protonate, if available

• Multiple small changes and cleanup

v1.2.3:

• Added support for Lipid21 sphingolipids

• Add channel_plug flag and fix 2LPG head atoms in memgen.parm

• Add function to identify sterol lipid piercing within packed box

• Limit packing of sterols in the rim under some conditions

v1.2.1:

• Fixed using %v/v concentrations for solutes.

v1.2.0:

• Added sterols ergosterol, stigmasterol, sitosterol, campesterol

• Reformated and cleaned FF parameter files

• Fixed bogus packing params

• Added functionality for using alternate solvents

• User provided memgen.parm or solvent.parm extend and not only replace parameters used by default

• Added support for coarse graining systems with SIRAH

• Fixed bug that caused charmmlipid2amber to fail when packing a single residue molecule

• Support for Lipid21 / Lipid17 can be selected.

v1.1.0:

• Added parameters for cardiolipin headgroup

• New PDBs generated with stereocenter constraints

• Added –solute_prot_dist to set free diffusion simulations with ligands starting at a distance of a potential target.

• Fixed rounding error for solute placement in water compartments

• Added flags –apl_offset –self_assembly

• Small code changes

v1.0.8:

• Added preliminary code for –double_span option for proteins with two transmembrane regions. Can be used with –preoriented given proper MEM atoms

• Added preliminary code for using different surface geometries

• Added –tight_box to use dimensions calculated during the packing process in the leap parametrization

v1.0.7:

• Added APL values derived from Lipid17 DOPC:X 4:1 300K 1 bar. Flag to use old APL values added.

• Allow to pass custom memgen.parm file with –memgen_parm

v1.0.5:

• Changed pdb file distro

• Added experimental pdbs for all possible combinations

• Added PI & multiple protonation states parameters

• memgen.parm to all missing lipids

v1.0.2:

• Fixed the way dims and solute_inmem are handled

• Included parameters for lysophospholipid heads PE PG PC // BETA! (pdbs and memgen.parm)

• Fixed and updated internal charmmlipid2amber.csv

• Added missing MG pdb

v1.0.1:

• Added flags dims, gaff2 and solute_charge

• Possible to specify concentrations as percentages. Depends on pdbremix at the moment!

v1.0.0:

• Modified POPC pdb to avoid bug that apparently caused it to be stuck in a maxima

• Fixed bug while trying to find lipid APL with the same headgroup

• Newest packmol version 18.169

• Inclusion of boost 1.69 // compatible with gcc 8 compilers // AmberTools19 includes boost!

• Mac compatible compilation code

v0.9.95:

• Added writeout flag to control intermediate saves. Allows shorter nloops.

• Adapted code to Leandro’s nloop_all.

• New packmol version with bug fixes (18.104). Should fix isues with Windows WSL.

• Python 3 friendly code.

• Added cubic flag for solvating. reducebuild for protonating HIS.

• Fixed multi bilayer z-dim size bug.

• Changed solute_con to accept either number of molecules or concentrations.

v0.9.9:

• Possibility to build stacked membrane systems by calling –lipids multiple times. PDB files to be embeded have to be included with –pdb now, to make possible to specify multiple inputs.

• A charge imbalance can be specified between compartments (CompEL!)

• If desired, a specific per leaflet composition can be specified.

• The orientation by MEMEMBED is with the N-terminus to the “inside” (or to lower z values). Added flag (–n_ter) to set this per protein in case of multiple bilayers.

v0.9.8:

• Modified print commands for logging statements.

• Added optional grid building command (testing!)

• Added functions that allow minimization and parametrization, given that AMBERHOME is defined

• Added option to keep ligands after protein alignment

v0.9.7:

• Check if ions are required before adding the line to packmol (avoids “bug” that adds one molecule even when the number is 0)

v0.9.6:

• Possible to add solutes in water based on PDB input

• Modified sigterm command for runs

• Reduced the verbosity. Can be called with –verbose

v0.9.5:

• Changed parsing system to argparse

• Adapted to work with Wooey

• Implemented charmmlipid2amber as a module // charmm and amber outputs

v0.9.1:

• Now is possible to create membranes without proteins by setting the PDB as None

• The xy dimensions can be set with the flag -distxy_fix. This flag is required if no PDB is given

v0.9:

• Multiple lipids available! (-available_lipids for a list)

• Detection of neutralization / salt concentration included

v0.7:

• Volume estimation by building grid based on PDBREMIX

• Search for AMBERHOME definition, using reduce if available

• Automated alignment available based on MEMEMBED

• Tiny code clean-up

v0.3:

• Distance is measured considering worst case scenario (max x and y considered to be on the diagonal)

• Added progress bar for all-together packing step

• Filter for non-defined arguments