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Binding free energy calculations in multicomponent systems

This example calculates the binding free energy of a multicomponent receptor-ligand system containing protein, RNA, magnesium ions, and a small-molecule ligand using the single-trajectory (ST) approximation.

  • Protocol

    Single trajectory

  • System

    Protein-RNA-ion-small-molecule complex

  • Solvent model

    GB-Neck2 (igb=8)

  • Bundled test

    gmx_MMPBSA_test -t 9

Before you begin

The manual workflow uses the following files and selections:

  • Calculation settings

    mmpbsa.in (-i)

  • GROMACS system

    Structure com.tpr (-cs) and topology topol.top (-cp). Keep the toppar directory containing the referenced *.itp files beside topol.top.

  • Trajectory

    PBC-corrected and fitted trajectory com_traj.xtc (-ct)

  • Molecular selections

    Index index.ndx (-ci) with the Protein_MG_RNA receptor group and TPP ligand group (-cg)

The topology must include the complete multicomponent system, including the TPP ligand and magnesium ions. A complex reference structure without hydrogens may also be supplied with -cr; it is optional but recommended when you need specific chain IDs or residue numbering. See the complete command-line reference for all options.

Run the example

Run the bundled test

The quickest way to reproduce this example is through the test runner:

gmx_MMPBSA_test -t 9

See the gmx_MMPBSA_test documentation for download, selection, and cleanup options.

Run it manually

Download the multicomponent example as a ZIP archive.

Extract the archive, change to the Comp_receptor directory, and choose either the serial or MPI command. You can also view the example files on GitHub before downloading them.

gmx_MMPBSA -O \
  -i mmpbsa.in \
  -cs com.tpr \
  -ct com_traj.xtc \
  -ci index.ndx \
  -cg Protein_MG_RNA TPP \
  -cp topol.top \
  -o FINAL_RESULTS_MMPBSA.dat \
  -eo FINAL_RESULTS_MMPBSA.csv

mpirun -np 2 gmx_MMPBSA -O \
  -i mmpbsa.in \
  -cs com.tpr \
  -ct com_traj.xtc \
  -ci index.ndx \
  -cg Protein_MG_RNA TPP \
  -cp topol.top \
  -o FINAL_RESULTS_MMPBSA.dat \
  -eo FINAL_RESULTS_MMPBSA.csv

Configure the calculation

The example uses the minimal mmpbsa.in shown first below. The all-options version was generated with gmx_MMPBSA --create_input gb and then adapted with the example-specific values. The concise block is the runnable starting point; the generated block exposes additional options and defaults, so the two blocks are not textually identical.

mmpbsa.in
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Sample input file for GB calculation
# This sample input is intended only to demonstrate that gmx_MMPBSA works.
# Although it follows the recommendations in the Amber manual, some parameters have been adjusted
# to keep computational cost reasonable. Modify them as appropriate for your system.

&general
sys_name="Complex_receptor",
PBRadii=4
/
&gb
igb=8, saltcon=0.150, intdiel=10
/
mmpbsa.in generated with --create_input gb
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Input block generated for the 1.7.0 release and adapted for this example.
Be careful with the variables you modify, some can have severe consequences on the results you obtain.

# General namelist variables
&general
  sys_name                       = "Multicomponent_receptor"                    # System name; e.g. "complex"
  startframe                     = 1                                      # First frame; e.g. 1
  endframe                       = 9999999                                # Last frame; e.g. 100
  interval                       = 1                                      # Frame interval; e.g. 1

  PBRadii                        = 4                                      # PB radii set; 1-7
  temperature                    = 298.15                                 # Temperature (K); e.g. 298.15
  qh_entropy                     = 0                                      # Legacy QH output reader; new calculations reject 1
  interaction_entropy            = 0                                      # Run IE entropy; 0/1
  ie_segment                     = 25                                     # IE tail diagnostic only (%); not primary IE; e.g. 25
  c2_entropy                     = 0                                      # Run C2 entropy; 0/1
  assign_chainID                 = 0                                      # Assign chain IDs; 0/1
  exp_ki                         = 0.0                                    # Experimental Ki (nM); e.g. 0.0
  full_traj                      = 0                                      # Write full trajectory; 0/1
  gmx_path                       = ""                                     # GROMACS path; e.g. "/usr/bin"
  keep_files                     = 2                                      # Files to keep; 0-2
  netcdf                         = 0                                      # Use NetCDF; 0/1
  solvated_trajectory            = 1                                      # Clean solvated traj.; 0/1
  explicit_waters                = 0                                      # Explicit waters; e.g. 10
  explicit_waters_mask           = "dASA"                                     # Water reference; e.g. ":1-10", "within 4", "dASA"
  explicit_waters_group          = "automatic"                                     # Solvent group; e.g. "TIP3" or "automatic"
  explicit_waters_dasa_cutoff    = 0.5                                    # dASA cutoff; e.g. 0.5
  explicit_waters_as             = "receptor"                             # Water owner; e.g. "receptor"
  explicit_waters_extra_points   = "error"                                # Virtual sites; "error" or "strip"
  verbose                        = 1                                      # Output verbosity; 0-2
/

# (AMBER) Generalized-Born namelist variables
&gb
  igb                            = 8                                      # GB model, e.g. 2 or 8
  intdiel                        = 10.0                                   # Internal dielectric; e.g. 1.0
  extdiel                        = 78.5                                   # External dielectric; e.g. 78.5
  saltcon                        = 0.150                                  # Salt conc. (M); e.g. 0.150
  surften                        = 0.0072                                 # Surface tension; e.g. 0.0072
  surfoff                        = 0.0                                    # Surface offset; e.g. 0.0
  molsurf                        = 0                                      # Use molsurf; 0/1
  msoffset                       = 0.0                                    # Molsurf offset; e.g. 0.0
  probe                          = 1.4                                    # Probe radius (A); e.g. 1.4
  ifqnt                          = 0                                      # Enable QM/MM; 0/1
  qm_theory                      = "PM6-DH+"                              # QM theory; e.g. "PM6-DH+"
  qm_residues                    = ""                                     # QM residues; e.g. ":1-5"
  com_qmmask                     = ""                                     # Complex QM mask; e.g. ":1-5"
  rec_qmmask                     = ""                                     # Receptor QM mask; e.g. ":1-5"
  lig_qmmask                     = ""                                     # Ligand QM mask; e.g. ":1"
  qmcharge_com                   = 0                                      # Complex QM charge; e.g. 0
  qmcharge_lig                   = 0                                      # Ligand QM charge; e.g. 0
  qmcharge_rec                   = 0                                      # Receptor QM charge; e.g. 0
  qmcut                          = 9999.0                                 # QM cutoff (A); e.g. 9999
  scfconv                        = 1e-08                                  # SCF convergence; e.g. 1.0e-8
  itrmax                         = 1000                                   # Maximum SCF iterations; e.g. 5000
  # ndiis_attempts                 = None                                 # Maximum DIIS attempts per SCF cycle; e.g. 700
  peptide_corr                   = 0                                      # Peptide correction; 0/1
  writepdb                       = 1                                      # Write QM PDB; 0/1
  verbosity                      = 0                                      # QM/MM verbosity; 0-5
  alpb                           = 0                                      # Use ALPB; 0/1
  arad_method                    = 1                                      # ALPB size method; e.g. 1
/

Keep in mind

This input provides a practical starting point and can serve as the basis for production calculations. Review the available input-file options, their accepted values, and adjust settings that depend on your system or protocol. Additional sample inputs are available here.

How this example works

The ST approximation reads the complex simulation and extracts the receptor and ligand components from every selected frame. Protein_MG_RNA selects the protein, RNA, and magnesium ions, while TPP selects the small-molecule ligand. This keeps all components conformationally matched during the calculation.

The bundled trajectory contains ten minimization frames. The calculation uses GB-Neck2 (igb=8), mbondi3 radii (PBRadii=4), an internal dielectric constant of 10, and a salt concentration of 0.15 M. This is a runnable regression/example input rather than a production sampling protocol.

Expected outputs

A successful calculation produces:

  • FINAL_RESULTS_MMPBSA.dat: the MM/GBSA summary and binding-energy statistics.
  • FINAL_RESULTS_MMPBSA.csv: the per-frame energy terms requested with -eo.

Analyze the results

Open the results with gmx_MMPBSA_ana for interactive inspection and plotting. See the gmx_MMPBSA_ana documentation for usage details.

Last update: September 13, 2026 05:57:32
Created: October 17, 2020 22:44:10
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