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AMBER input files binding free energy calculations

Info

This example can be found in the examples/AMBER directory in the repository folder. If you didn't use gmx_MMPBSA_test before, use downgit to download the specific folder from gmx_MMPBSA GitHub repository.

Requirements

In this case, amber_MMPBSA requires:

Input File required Required Type Description
Input parameters file in Input file containing all calculation specifications
Complex topology file prmtop AMBER topology file for the complex
Complex structure file inpcrd AMBER coordinate file for the complex
Complex trajectory file mdcrd AMBER trajectory file for the complex
Receptor and ligand masks masks AMBER masks identifying the receptor and ligand in the complex
Receptor topology file prmtop AMBER topology file for the receptor
Ligand topology file prmtop AMBER topology file for the ligand

-> Must be defined -- -> Optional

See a detailed overview of amber_MMPBSA inputs and flags here.

Command-line

Once you are in the folder containing all files, the command-line will be as follows:

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

gmx_MMPBSA_test -t 25

where the mmpbsa.in input file is a text file containing the following lines:

Sample input file for AMBER input files
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Input file for a short AMBER input files test
&general
   sys_name="AMBER",
   startframe=1,
   endframe=5,
   interval=1,
   verbose=1,
/
&gb
   igb=2, saltcon=0.100,
/

Keep in mind

This example is meant only to show that amber_MMPBSA works with native AMBER input files. It uses a short five-frame trajectory and preserves the radii already stored in the AMBER topology files.

Considerations

In this case, a single trajectory (ST) approximation is followed. The receptor and ligand are selected from the complex with AMBER masks (:1-166 and :167-242). Receptor and ligand topology files are provided directly, so amber_MMPBSA can build the working topologies without using GROMACS files.

Last update: July 12, 2026 09:08:00
Created: July 11, 2026 06:19:03
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