Biocad Tool

Molecular parametrization pipeline for GROMACS using OpenFF

This tool converts ligand structures from an SDF file into:

• .gro structures (GROMACS format)
• .top topology files (OpenFF SMIRNOFF-based)

It supports multiple conformers and parallel processing.

Input

• SDF file containing ligand structures with 3D coordinates

Example:

file.sdf

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Output

For each unique molecule:

outdir/
  MOLECULE_NAME/
    topol.top
    conf_0.gro
    conf_1.gro
    ...

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Usage

Command line

python biocad_tool.py --sdf file.sdf --out outdir --nproc 4 --log run.log

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Arguments

Argument	Description
--sdf	Path to input SDF file
--out	Output directory
--nproc	Number of CPU cores
--log	Log file path

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Requirements

All requirements are in environment.yaml

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Author

Matvei Beliakov

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P.S.

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