Usage

This document details the various functions and usage methods of s_mmpbsa to help you deeply understand and fully utilize this tool for binding free energy calculations.

Command Line Parameters

s_mmpbsa supports the following command line parameters:

# Basic usage
s_mmpbsa [options] [tpr file]

# Options
--version   Display version information

Interactive Command Line Interface

s_mmpbsa’s interactive command line interface is divided into the following main parts:

  1. File loading: Load tpr, xtc and ndx files

  2. Trajectory parameter setting: Set receptor, ligand groups, time interval, etc.

  3. MM-PBSA parameter setting: Set various parameters related to calculation

  4. Calculation execution: Execute MM-PBSA calculation

  5. Result analysis: Analyze and visualize calculation results

The operation methods and parameter settings of each part are described in detail below.

File Loading

After starting s_mmpbsa, you first need to load the necessary input files:

  • tpr file: Gromacs topology parameter file, containing system topology information and atomic parameters

  • xtc file: Gromacs trajectory file, containing system coordinate information

  • ndx file: Gromacs index file, containing system grouping information

Example operations for loading files:

# Input tpr file path (can be absolute or relative path)
md.tpr

# Choose to load xtc file
1
md_centered.xtc  # Input xtc file path, press Enter to use default md.xtc

# Choose to load ndx file
2
index.ndx  # Input ndx file path, press Enter to use default index.ndx

# Proceed to next step
0

Trajectory Parameter Setting

After loading files, you need to set trajectory parameters, mainly including:

  • Receptor group: Choose which group to use as the receptor

  • Ligand group: Choose which group to use as the ligand

  • Time interval: Set the time interval for analysis

  • Skipped frames: Set the number of frames to skip before starting analysis

  • End analysis time point: Set the time point to end analysis

Example operations for setting trajectory parameters:

# Select receptor group
1
1  # Input the number of the receptor group, for example 1 represents Protein group

# Select ligand group
2
13  # Input the number of the ligand group, for example 13 represents ligand

# Set start time
3
0  # Input the number of frames to skip, default is 0

# Set end time
4
0  # Input end time point, 0 means analyze until the end of the trajectory

# Set time interval (unit: ns)
5
1  # Input time interval, for example 1 means analyze once every 1ns

# Proceed to next step
0

MM-PBSA Parameter Setting

Next, set the relevant parameters for MM-PBSA calculation. s_mmpbsa provides multiple parameter setting options:

# Display current parameter settings
1

# Set temperature (unit: K)
2
298.15  # Input temperature, default is 298.15K

# Set NaCl concentration (unit: mol/L)
3
0.15  # Input KCl concentration, default is 0.15mol/L

# Set salt bridge search distance (unit: Å)
4
4.0  # Input salt bridge search distance, default is 4.0Å

# Set hydrogen bond search distance (unit: Å)
5
3.5  # Input hydrogen bond search distance, default is 3.5Å

# Set van der Waals cutoff distance (unit: Å)
6
14.0  # Input van der Waals cutoff distance, default is 14.0Å

# Set number of parallel cores for MM calculation
7
4  # Input number of parallel cores, default is the number of system CPU cores

# Set PB parameters
8
# Enter PB parameter setting submenu (see below for details)

# Set SA parameters
9
# Enter SA parameter setting submenu (see below for details)

# Proceed to next step
0

PB Parameter Setting

In the PB parameter setting submenu, you can set the following parameters:

# Display current PB parameter settings
1

# Set solvent dielectric constant
2
78.54  # Input solvent dielectric constant, default is 78.54

# Set solute dielectric constant
3
1.0  # Input solute dielectric constant, default is 1.0

# Set grid spacing (unit: Å)
4
0.5  # Input grid spacing, default is 0.5Å

# Set APBS executable file path
5
/usr/local/bin/apbs  # Input APBS executable file path, press Enter to use built-in path

# Return to previous menu
0

SA Parameter Setting

In the SA parameter setting submenu, you can set the following parameters:

# Display current SA parameter settings
1

# Set surface tension (unit: kJ/(mol·Å²))
2
0.0379  # Input surface tension, default is 0.0379 kJ/(mol·Å²)

# Set non-polar solvation parameter (unit: kJ/(mol·Å³))
3
0.0  # Input non-polar solvation parameter, default is 0.0 kJ/(mol·Å³)

# Set SAS calculation method (0: Shrake-Rupley, 1: MSMS)
4
0  # Input SAS calculation method, default is 0 (Shrake-Rupley)

# Return to previous menu
0

Executing Calculation

After setting up, start executing the MM-PBSA calculation. Before calculation, you need to input the system name:

# Input system name
system  # Input system name, default is system

# A progress bar and current energy value will be displayed during calculation
# After calculation is complete, you will automatically enter analysis mode

Result Analysis

After calculation is complete, you can analyze the results. s_mmpbsa provides multiple analysis options:

# Generate pdb file containing residue binding energy information
-1
0  # Input time point, 0 means average value

# View result summary
1

# Output energy change data over time
2

# Output residue binding energy at a specific time point
3
0  # Input time point, 0 means average value
1  # Choose to output residues within 3Å range (0: all residues, 1: 3Å range, 2: 5Å range, 3: 10Å range)

# Output binding energy of ligand atoms
4

# Output hydrogen bond and salt bridge information
5

# Output interaction energy matrix
6

# Exit program
0

Using Analysis Mode

s_mmpbsa also provides a special analysis mode, which can re-analyze already calculated results without re-calculating:

# Start analysis mode
s_mmpbsa
a  # Input 'a' in the interactive interface to enter analysis mode

# Input working directory path
./results  # Input the directory containing .sm result files, default is current directory

# Input temperature (unit: K)
298.15  # Input temperature, default is 298.15K

# Input system name
system  # Input the system name used during previous calculation, default is system

# Subsequent analysis operations are the same as after normal calculation completion

Alanine Scanning

s_mmpbsa also supports alanine scanning function, which can systematically mutate protein residues to alanine and calculate the binding free energy change before and after mutation.

Steps for performing alanine scanning:

# Prepare working directory
mkdir -p ala_scan
cd ala_scan

# Copy necessary input files
cp ../md.tpr ../md_centered.xtc ../index.ndx .

# Execute alanine scanning
s_mmpbsa md.tpr
1
md_centered.xtc
2
index.ndx
0
1
1  # Select receptor group (protein)
2
13  # Select ligand group
5
1
0
0
system  # System name
-1  # Generate pdb file (optional)
0  # Exit analysis
a  # Enter analysis mode
.  # Use current directory
298.15  # Temperature
system  # System name
0  # Exit analysis

# Now you can view the results of alanine scanning

Interpretation of Calculation Results

s_mmpbsa’s calculation results mainly include the following energy terms:

  • ΔG_bind: Total binding free energy

  • ΔH: Enthalpy change

  • TΔS: Entropy contribution (Note: s_mmpbsa does not directly calculate entropy at present, this value is usually set to 0 or estimated through other methods)

  • ΔE_vdw: Van der Waals interaction energy

  • ΔE_elec: Electrostatic interaction energy

  • ΔG_polar: Polar solvation free energy

  • ΔG_nonpolar: Non-polar solvation free energy

A larger negative value of binding free energy indicates stronger binding. Usually, ΔG_bind < -10 kJ/mol indicates strong binding.

Notes

When using s_mmpbsa, you need to pay attention to the following points:

  1. Trajectory quality: Ensure good trajectory quality, with correct PBC handling, centering and fitting operations.

  2. Index file: Ensure that the index file contains correct receptor and ligand groups.

  3. Parameter selection: For different systems, parameters may need to be adjusted to obtain more accurate results.

  4. Parallel computing: Setting an appropriate nkernels value in settings.ini can utilize multi-core CPU to accelerate calculation.

  5. Result verification: It is recommended to compare with experimental data or results from other calculation methods to verify the reliability of calculation results.

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