Command-line

// All flags available in `gmx_MMPBSA` are shown below:

$ gmx_MMPBSA -h

usage: gmx_MMPBSA [-h] [-v] [--input-file-help]
                  [--create_input [{gb,pb,pb_mem,rism,ala,decomp,nmode,gbnsr6,all} ...]]
                  [-O] [-prefix <file prefix>] [-sys_name <system name>]
                  [--progress-style {auto,rich,classic,plain,none}] [-i FILE] [-xvvfile XVVFILE] [-o FILE]
                  [-do FILE] [-eo FILE] [-deo FILE] [-nogui] [-s] [--no-error-bundle] [-cs <Structure File>]
                  [-ci <Index File>] [-cg group group]
                  [-ct [TRJ ...]] [-cp <Topology>] [-cr <PDB File>] [-rs <Structure File>] [-ri <Index File>]
                  [-rg group] [-rt [TRJ ...]] [-rp <Topology>] [-lm <Structure File>] [-ls <Structure File>]
                  [-li <Index File>] [-lg group] [-lt [TRJ ...]] [-lp <Topology>] [--rewrite-output] [--clean]

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state 
free energy calculations with GROMACS files. This program is an adaptation of 
Amber's MMPBSA.py and essentially works as such. gmx_MMPBSA works with any GROMACS version.
This program will calculate binding free energies using end-state free energy methods 
on an ensemble of snapshots using a variety of implicit solvent models. This is the core 
of gmx_MMPBSA and it will do all the calculations

options:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  --input-file-help     Print all available options in the input file. (default: False)
  --create_input [{gb,pb,pb_mem,rism,ala,decomp,nmode,gbnsr6,all} ...]
                        Create an new input file with selected calculation
                        type. (default: None)

Miscellaneous Options:
  -O, --overwrite       Allow output files to be overwritten (default: False)
  -prefix <file prefix> Prefix for intermediate files. (default: _GMXMMPBSA_)
  -sys_name <system name>, --sys_name <system name>
                        System name. Overrides sys_name in the input file.
                        (default: None)
  --progress-style {auto,rich,classic,plain,none}
                        Calculation progress display. Auto uses Rich in a
                        terminal and classic otherwise. (default: auto)

Input and Output Files:
  These options specify the input files and optional output files.

  -i FILE               MM/PBSA input file. (default: None)
  -xvvfile XVVFILE      XVV file for 3D-RISM. (default: installed bundled
                         GMXMMPBSA/data/xvv_files/tip3p.xvv, unless the
                         legacy AMBERHOME XVV file is available)
  -o FILE               Output file with MM/PBSA statistics.
                         (default: FINAL_RESULTS_MMPBSA.dat)
  -do FILE              Output file for decomposition statistics summary.
                         (default: FINAL_DECOMP_MMPBSA.dat)
  -eo FILE              CSV-format output of all energy terms for every frame in
                         every calculation. Defaults to the .csv counterpart of
                         the file specified with -o; use -eo to override its name.
                         (default: derived from -o)
  -deo FILE             CSV-format output of all energy terms for each printed
                         residue in decomposition calculations. Defaults to the
                         .csv counterpart of the file specified with -do; use -deo
                         to override its name. (default: derived from -do)
  -nogui                No open gmx_MMPBSA_ana after all calculations finished
                         (default: True)
  -s, --stability       Perform stability calculation. Only the complex parameters
                         are required. Receptor and ligand parameters are ignored.
                         (default: False)
  --no-error-bundle     Do not create a diagnostic zip bundle automatically when
                         gmx_MMPBSA fails. (default: False)

Complex:
  Complex files and info that are needed to perform the calculation. If the
  receptor and/or the ligand info is not defined, we generate them from that of
  the complex.

  -cs <Structure File>  Structure file of the complex. Allowed formats: *.tpr
                         (recommended), *.pdb (default: None)
  -ci <Index File>      Index file of the bound complex. (default: None)
  -cg group group       Receptor and ligand groups in the complex index file,
                        specified by zero-based group number or group name. For
                        example: -cg 1 13 or -cg Protein LIG
                         (default: None)
  -ct [TRJ ...]         Complex trajectories. Make sure the trajectory is
                        fitted and pbc have been removed. Allowed formats:
                        *.xtc (recommended), *.trr, *.pdb (specify as many as
                        you'd like). (default: None)
  -cp <Topology>        Required GROMACS complex topology (*.top). Parameters
                         are converted with ParmEd; structure-only tleap
                         rebuilds are not supported. Small-molecule ligands
                         must be included in this topology. (default: None)
  -cr <PDB File>        Complex Reference Structure file. This option is optional
                         but recommended (Use the PDB file used to generate the 
                         topology in GROMACS). If not defined, the chains ID 
                         assignment (if the structure used in -cs does not have 
                         chain IDs) will be done automatically according to the 
                         structure (can generate wrong mapping). (default: None)

Receptor:
  Receptor files and info that are needed to perform the calculation. If the
  receptor info is not defined, we generate it from that of the complex.

  -rs <Structure File>  Structure file of the unbound receptor for multiple
                         trajectory approach. Allowed formats: *.tpr (recommended),
                         *.pdb (default: None)
  -ri <Index File>      Index file of the unbound receptor. (default: None)
  -rg group             Receptor group in the receptor index file, specified by
                         zero-based group number or group name. For example: -rg 1
                         or -rg Protein (default: None)
  -rt [TRJ ...]         Input trajectories of the unbound receptor for
                        multiple trajectory approach. Allowed formats: *.xtc
                        (recommended), *.trr, *.pdb (specify as many as
                        you'd like). (default: None)
  -rp <Topology>        GROMACS topology of the unbound receptor. Required with
                         -rs/-rt (MT). (default: None)

Ligand:
  Ligand files and info that are needed to perform the calculation. If the ligand
  are not defined, we generate it from that of the complex.

  -lm <Structure File>  Deprecated. Ignored when -cp is used. Small-molecule
                         ligands must be present in the GROMACS topology
                         (-cp / -lp). (default: None)
  -ls <Structure File>  Structure file of the unbound ligand for multiple
                         trajectory approach. Allowed formats: *.tpr
                         (recommended), *.pdb (default: None)
  -li <Index File>      Index file of the unbound ligand. Only if tpr file was
                         define in -ls. (default: None)
  -lg group             Ligand group in the ligand index file, specified by zero-
                         based group number or group name. For example: -lg 13 or
                         -lg LIG (default: None)
  -lt [TRJ ...]         Input trajectories of the unbound ligand for multiple
                        trajectory approach. Allowed formats: *.xtc
                        (recommended), *.trr, *.pdb (specify as many as
                        you'd like). (default: None)
  -lp <Topology>        GROMACS topology of the unbound ligand. Required with
                         -ls/-lt (MT). (default: None)

Miscellaneous Actions:
  -rewrite-output       Do not re-run any calculations, just parse the output
                         files from the previous calculation and rewrite the
                         output files. (default: False)
  --clean               Clean temporary files and quit. (default: False)

gmx_MMPBSA is an effort to implement the GB/PB and others calculations in
GROMACS. Based on MMPBSA.py (version 14.0) and AmberTools 26.0 and GROMACS
2026.0