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amber_MMPBSA

amber_MMPBSA is an independent command-line module included with gmx_MMPBSA for running end-state free energy calculations directly from native AMBER input files.

Unlike gmx_MMPBSA, which prepares and processes GROMACS files before building the AMBER-compatible calculation workflow, amber_MMPBSA starts from AMBER topology, coordinate, trajectory, and mask inputs. This makes it useful when the system has already been prepared in the AMBER ecosystem and no GROMACS files are needed.

Although amber_MMPBSA is an independent module, the calculation and analysis features available in gmx_MMPBSA also work with amber_MMPBSA workflows. This includes the same input file options for supported calculation types, output generation, decomposition analysis, entropy calculations, CSV export, result rewriting, and post-processing with gmx_MMPBSA_ana.

Input files

amber_MMPBSA uses native AMBER files:

Input Option Description
Complex topology -cp AMBER topology file for the complex
Complex structure -cs AMBER coordinate file for the complex. Supported formats include *.pdb, *.inpcrd, and *.rst7
Complex trajectory -ct AMBER trajectory file. Supported format: *.mdcrd
Complex masks -cm Receptor and ligand masks from the complex
Receptor topology -rp AMBER topology file for the receptor
Ligand topology -lp AMBER topology file for the ligand

Example

A basic single-trajectory command is:

amber_MMPBSA -O -i mmpbsa.in \
  -cp ras-raf_complex.prmtop \
  -cs ras-raf_complex.inpcrd \
  -ct prod_complex.mdcrd \
  -cm ":1-166" ":167-242" \
  -o FINAL_RESULTS_MMPBSA.dat \
  -eo FINAL_RESULTS_MMPBSA.csv

See the AMBER input files example for a complete runnable example.

Last update: July 11, 2026 19:15:33
Created: July 11, 2026 19:15:33
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