GROMACS to CHARMM Force Field Converter

This repository contains scripts for converting GROMACS force field parameters to CHARMM format and tools for structure validation.

Updates

July 28, 2025

• Fixed force constant conversion in convert_to_charmm.sh for bond and angle parameters.
• In GROMACS, bond and angle energies are calculated as V(x) = kx²/2, while CHARMM uses V(x) = kx².
• Updated conversion factors to divide bond and angle force constants by 2 when converting from GROMACS to CHARMM format.
• Added Urey-Bradley (UB) terms support to angle parameter conversion.
• GROMACS angle format: atom1 atom2 atom3 func θ0 kθ S0 KUB
• CHARMM angle format: atom1 atom2 atom3 Kθ θ0 KUB S0
• KUB force constants use bond force constant conversion (including divide by 2 from GROMACS to CHARMM).
• S0 distances use length conversion (nm to Å).

Citation

The force field files used in this repository are from:

CHARMM-DYES: Parameterization of Fluorescent Dyes for Use with the CHARMM Force Field
Cite this: J. Chem. Theory Comput. 2020, 16, 12, 7817–7824

The original force field files (ffdyes.itp, ffdyesbonded.itp, ffdyesnonbonded.itp, and merged.rtp) were developed as part of the CHARMM-DYES force field. This repository provides tools to convert these parameters between GROMACS and CHARMM formats.

Scripts

1. convert_to_charmm.sh

This script converts GROMACS ITP files to CHARMM PRM format. It handles the conversion of:

• ATOMS (mass definitions)
• BONDS (bond parameters)
• ANGLES (angle parameters)
• DIHEDRALS (proper and improper dihedral parameters)
• NONBONDED (Lennard-Jones parameters)

Usage:

./convert_to_charmm.sh

The script provides an interactive menu for:

• Configuring input/output files
• Setting conversion factors
• Selecting which sections to process
• Reviewing settings before conversion

Input Files:

• parameters/forcefield/charmm36_dyes.ff/ffdyesnonbonded.itp
• parameters/forcefield/charmm36_dyes.ff/ffdyesbonded.itp
• parameters/forcefield/charmm36_dyes.ff/ffdyes.itp

Output:

• dyes.prm (default name, configurable) - Example output file containing converted CHARMM parameters

2. generate_str.sh

This script generates CHARMM stream files (.str) from GROMACS RTP files and PDB structures. It:

• Scans RTP files for available residues
• Allows interactive selection of residues
• Generates topology and parameter files
• Handles bonds, angles, dihedrals, and impropers

Usage:

./generate_str.sh

The script will:

1. Show available residues
2. Prompt for residue selection
3. Search for corresponding PDB files
4. Generate STR and temporary PRM files

Input Files:

• parameters/forcefield/charmm36_dyes.ff/merged.rtp
• PDB files in parameters/forcefield/pdbs/dyes/ or parameters/forcefield/pdbs/with_linker/

Output:

• [residue_name].str - Example: CY7.str contains the CHARMM stream file for the CY7 dye molecule
• [residue_name].tem.prm - Temporary parameter file used during generation

3. combine_str.sh

This script combines two CHARMM stream files (.str) into a single structure. It:

• Allows deletion of specific atoms from either structure
• Creates new bonds between the two structures
• Maintains proper atom naming and numbering
• Preserves all comments and parameter sections

Usage:

./combine_str.sh

The script will:

1. Prompt for two input STR files
2. Ask for a 4-character residue name for the combined structure
3. Allow specification of atoms to delete from each structure
4. Enable creation of new bonds between the structures
5. Generate a combined STR file with proper formatting

Example:

• Input files: CY3.str and CY7.str
• Output file: CY3_CY7_combine.str - Contains the combined structure with proper atom naming and bonds

Features:

• Preserves comments from both original files
• Maintains proper atom numbering
• Combines parameter sections (BONDS, ANGLES, DIHEDRALS, IMPROPERS)
• Removes duplicates in parameter sections
• Adds clear documentation of which files were combined

Example Output Files

The repository includes example output files to demonstrate the conversion results:

1. dyes.prm: CHARMM parameter file generated by convert_to_charmm.sh, containing:

   • Mass definitions
   • Bond parameters
   • Angle parameters
   • Dihedral parameters (both proper and improper)
   • Nonbonded parameters

2. CY7.str: CHARMM stream file generated by generate_str.sh for the CY7 dye molecule, containing:

   • Residue topology
   • Atom definitions
   • Bond connections
   • Improper dihedral definitions

3. CY3_CY7_combine.str: CHARMM stream file generated by combine_str.sh, demonstrating:

   • Combined structure of CY3 and CY7 dyes
   • Proper atom naming and numbering
   • New bonds between the structures
   • Combined parameter sections

Bond Sanity Check Tool

This repository contains tools for checking and validating molecular structure files.

Bond Sanity Check Script (bond_sanity_check.sh)

This script performs a sanity check between STR (structure) and PRM (parameter) files by verifying that all bond definitions in the STR file have corresponding parameter definitions in the PRM files.

Features

• Interactive prompts for input files
• Checks all BOND definitions in the STR file
• Maps atoms to their atom types using ATOM definitions
• Verifies bond parameters exist in PRM files
• Shows the first 5 missing bonds automatically
• Option to view additional missing bonds
• Displays both original atom names and their corresponding atom types

Usage

1. Make sure the script is executable:

   chmod +x bond_sanity_check.sh

2. Run the script:

   ./bond_sanity_check.sh

3. When prompted:

   • Enter the path to your STR file
   • Enter the paths to one or more PRM files
   • Press Enter without input when done adding PRM files

Output Format

For each missing bond, the script outputs:

Missing bond: ATOM1 ATOM2 (TYPE1 TYPE2)

Where:

• ATOM1 ATOM2: Original atom names from the STR file
• TYPE1 TYPE2: Corresponding atom types from the ATOM definitions

If there are more than 5 missing bonds, the script will prompt:

Show next 5 missing bonds? (y/n)

This repeats in groups of 5 until all missing bonds are shown or you choose to stop.

Example

$ ./bond_sanity_check.sh
Bond Sanity Check Script
=======================
Enter the path to the STR file: molecule.str
Enter the path to a PRM file (or press Enter to finish): params1.prm
Enter the path to a PRM file (or press Enter to finish): params2.prm
Enter the path to a PRM file (or press Enter to finish): 

Missing bond: C1 C2 (CG2R61 CG2R61)
...

Requirements

• Bash shell
• Basic Unix tools (awk, grep)
• Read permissions for input files

File Structure

.
├── Scripts/                    # Conversion and validation scripts
│   ├── convert_to_charmm.sh   # Converts GROMACS parameters to CHARMM format
│   ├── generate_str.sh        # Generates CHARMM stream files from RTP files
│   ├── combine_str.sh         # Combines two CHARMM stream files
│   ├── bond_sanity_check.sh   # Validates bond parameters between STR and PRM files
│   └── parse_rtp.sh          # Helper script for RTP file processing
│
├── Example_output/           # Example output files
│   ├── dyes.prm             # Converted CHARMM parameters
│   ├── CY3.str             # Example stream file for CY3
│   ├── CY7.str             # Example stream file for CY7
│   └── CY3_CY7_combine.str # Combined structure example
│
└── parameters/              # Input parameter files
    └── forcefield/         # GROMACS force field files
        ├── charmm36_dyes.ff/
        │   ├── ffdyesbonded.itp
        │   ├── ffdyesnonbonded.itp
        │   └── merged.rtp
        └── pdbs/
            └── dyes/
                └── cy7.pdb

Requirements

• Bash shell
• bc (for floating-point calculations)
• awk
• grep
• se

Unit Conventions and Conversion Factors

GROMACS Units

• Energy: kJ/mol
• Length: nm
• Bond force constant: kJ/mol/nm²
• Angle force constant: kJ/mol/rad²
• Dihedral force constant: kJ/mol
• Nonbonded parameters:
  • ε (epsilon): kJ/mol
  • σ (sigma): nm

CHARMM Units

• Energy: kcal/mol
• Length: Å
• Bond force constant: kcal/mol/Ų
• Angle force constant: kcal/mol/rad²
• Dihedral force constant: kcal/mol
• Nonbonded parameters:
  • ε (epsilon): kcal/mol
  • Rmin/2: Å

Default Conversion Factors

The scripts use the following conversion factors:

• Energy: 1 kJ/mol = 0.239005736 kcal/mol
• Length: 1 nm = 10 Å
• Bond force constant: 1 kJ/mol/nm² = 11.9502868 kcal/mol/Ų (divided by 2 for GROMACS→CHARMM)
• Angle force constant: 1 kJ/mol/rad² = 0.119502868 kcal/mol/rad² (divided by 2 for GROMACS→CHARMM)
• Dihedral force constant: 1 kJ/mol = 0.239005736 kcal/mol
• Nonbonded parameters:
  • ε: Convert using energy factor and make negative (CHARMM uses negative epsilon)
  • Rmin/2: σ × 2^(⅙)/2 = σ x 0.5612310241546865 (conversion from sigma to Rmin/2)

Note: Bond and angle force constants are divided by 2 when converting from GROMACS to CHARMM because GROMACS uses V(x) = kx²/2 while CHARMM uses V(x) = kx².

Working Directory

The 7_5_2025/ directory contains:

• STR files from ongoing work and development
• Notes and documentation for current projects
• Temporary working files and experimental data