Ligand Parameterization (GAFF / ACPype)

GAFF force-field parameters for a small molecule, ready for GROMACS.

by Temple Compute

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W-04 · Ligand Parameterization (GAFF / ACPype)

GAFF force-field parameters for a small molecule, ready for GROMACS.

Domain: BioExcel Building Blocks

Overview

Generates GROMACS parameters for a ligand with GAFF via ACPype. The ligand comes from a PDB ligand code (default IBP, ibuprofen) or an upload; OpenBabel adds hydrogens at the chosen pH and minimizes them. The workflow has 4 tasks.

Pipeline

fetch_ligand         Fetch ligand_code from the PDB, or use the uploaded ligand
add_hydrogens        Add hydrogens at the chosen pH (OpenBabel)
minimize_hydrogens   Minimize hydrogen positions (OpenBabel, GAFF)
parameterize         ACPype / GAFF parameters

Inputs / Outputs

Input: ligand_code or, when empty, the ligand upload.
Outputs: results/ligand.pdb, ligand.H.mol2, ligand.H.min.pdb, ligand.params.gro, ligand.params.itp, ligand.params.top.

Parameters

| id | Default | Meaning | |---|---|---| | ligand_code | IBP | PDB Chemical Component code; clear it to use ligand | | ligand | examples/ibp.pdb | Ligand used when ligand_code is empty (heavy atoms suffice) | | ph | 7.4 | pH for adding hydrogens | | net_charge | -1 | Formal net charge at that pH, passed to ACPype |

net_charge must match the ligand at the chosen pH, otherwise ACPype (AM1-BCC) fails or gives wrong charges.