TopFor

TopFor is a command-line tool for generating AMBER parameters for non-standard amino acids (NSAA). It automates capping, charge calculation, and parameter file creation for use with AMBER force fields.

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Features

• Single-file mode: Process one MOL2 file at a time
• Batch mode: Process multiple MOL2 files via a text file list
• Automated pipeline: Capping, Antechamber, TLeap, PREPGEN, and PARMCHK2 steps are chained automatically

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Requirements

• Operating System: Linux, macOS, or Windows with WSL/Git Bash
• AMBER Tools: antechamber, tleap, prepgen, parmchk2 installed and in your PATH
• Conda: Miniforge or Anaconda installed

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Installation

1. Clone the repository

git clone git@github.com:Heshine-G/TopFor.git
cd TopFor

2. Create and activate the conda environment

conda create -n paramgen python=3.10 numpy pandas rdkit pymol-open-source ambertools -c conda-forge
conda activate paramgen

3. Make the CLI launcher script executable

chmod +x topfor

4. Add the project directory to your PATH

echo 'export PATH="$PATH:$(pwd)"' >> ~/.bashrc
source ~/.bashrc

Note: If you clone elsewhere, replace $(pwd) with the absolute path.

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Usage

Single-file mode

topfor -i myresidue.mol2

Batch mode via text file list

1. Create a text file (e.g., list.txt) with one .mol2 path per line
2. Run:

topfor -b list.txt

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Flags

• -i, --input → Path to a single .mol2 file
• -b, --batch → Glob pattern or .txt file containing .mol2 paths

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Output

For each input file NAME.mol2, the tool creates a directory NAME/ containing:

• NAME.ac, NAME.mol2 → Charged structures
• NAME.lib → TLeap library
• NAME.prepin → PREPGEN input
• NAME.mc → MC file
• NAME.frcmod, NAME_GAFF.frcmod, NAME_FF14SB.frcmod → Parameter modification files

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Examples

# Single file
topfor -i AIB.mol2


# Batch via list
echo "AIB.mol2" > list.txt
echo "FGA.mol2" >> list.txt
topfor -b list.txt

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Troubleshooting

• bash: topfor: command not found
  Ensure:

  chmod +x topfor

  and your repo folder is added to PATH.

• CRLF errors
  Convert script to LF line endings:

  dos2unix topfor

  Or in VS Code: click the CRLF indicator (bottom-right) → select LF