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Introduction

easyPARM is a computational tool designed with six key functionalities:

1. Force Field Parameter Derivation for Metal-Containing Systems

easyPARM derives bond-stretching and bond-angle bending force field parameters for metal-containing molecular systems using the Seminario method. This ensures accurate parameter generation tailored for the AMBER software suite, based on the Hessian matrix produced by frequency calculation in Gaussian, Orca, or GAMESS software.

2. Force Field Parameterization for Metalloproteins

The tool facilitates the derivation of bond-stretching and bond-angle bending force field parameters for metalloproteins using the Seminario method. This capability streamlines the integration of these parameters into protein force fields.

3. Force Field Parameterization of Multi-Metal Metalloproteins

Our tool enables precise derivation of bond-stretching and bond-angle bending force field parameters for multi-metal metalloproteins through the Seminario method. This advanced capability seamlessly integrates these parameters into standard protein force fields, streamlining the generation of comprehensive parameter libraries.

4. Generation of CHARMM Force Field Parameter Format

easyPARM extends its capabilities to the CHARMM ecosystem by implementing the Seminario method for metal-containing systems. The tool processes Hessian matrices from Gaussian, Orca, or GAMESS quantum chemistry calculations to generate bond and angle parameters in native CHARMM format. For organic components, easyPARM seamlessly integrates parameters from the CGenFF force field, creating a complete parameter set for mixed metal-organic systems.

5. AMBER Format Conversion to GROMACS or OpenMM

easyPARM utilizes ParmEd to convert AMBER-format files into GROMACS or OpenMM formats, facilitating compatibility with other molecular dynamics engines.

6. Charge Restraints with REsP Fitting

easyPARM supports the application of charge restraints on specific atoms using the Restrained Electrostatic Potential (REsP) fitting approach. This helps achieve a more accurate electrostatic potential around the molecule while keeping the charge distribution physically meaningful.

7. Enhanced GAFF Atom Type Assignment

easyPARM provides advanced atom type assignment capabilities that accurately determine GAFF atom types even when Antechamber fails, particularly for complex multi metal-containing structures. Using sophisticated analysis of molecular topology, ring systems, hybridization states, and aromaticity, this functionality ensures precise atom typing that directly improves the quality of the resulting force field parameters.

Authors & License

The easyPARM code was written by Abdelazim M. A. Abdelgawwad under the supervision of Dr. Antonio Francés-Monerris.

This code (version 3.30) is free software: you can redistribute it and/or modify it under the GNU Lesser General Public License (LGPL) Version 2.1, February 1999.

Key Features

  • Generates parameters for metal-containing and multi-metal metalloprotein systems using a combination of the General AMBER Force Field (GAFF) and missing parameters for bond stretching and angle bending involving metals and coordinating atoms using the Seminario method.

  • Capable of generating parameters for entire structures in non-metal systems using GAFF or AMBER.

  • Supports parameter generation in CHARMM format, combining Seminario-derived metal-coordination parameters with organic components from the CGenFF force field, enabling simulations in CHARMM-compatible software.

  • Outputs essential files (frcmod, pdb, mol2, and lib for AMBER; prm, top for CHARMM) for initiating simulations or preparing metal-containing systems.

  • Facilitates cross-platform compatibility through ParmEd-based conversion to GROMACS and OpenMM formats.

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© 2025 Abdelazim M. A. Abdelgawwad. Distributed under the GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999.