Ligands

Ligand parameterization and CGenFF support

Small molecules need parameters that agree with the biomolecular force field. PyMACS supports practical CGenFF workflows while keeping ligand names and topology files aligned.

Canonical ligand files

File	Purpose
<LIG>.str	CGenFF stream file containing ligand parameters.
<LIG>.cgenff.mol2	CGenFF MOL2 file with atom names/types/charges.
<lig>.itp	Converted GROMACS include topology.
<lig>.prm	Converted ligand parameter file.
posre_<lig>.itp	Optional position-restraint include for the ligand.

Three supported modes

Mode	When to use it
Pre-converted GROMACS ligand files	You already have .itp/.prm/restraint files and want to import them.
CGenFF server outputs only	Recommended for many users: provide .str and .cgenff.mol2 and let PyMACS convert.
Local SILCSBio/CGenFF automation	Advanced local processing when the full local toolchain is available.

Common setup command

Copy command

cp Example_Choices/Example1/input/CPD32_9G94.pdb .
cp Example_Choices/Example1/parameters/A1D.str .
cp Example_Choices/Example1/parameters/A1D.cgenff.mol2 .
python 1_AutomateGromacs.py --pdb CPD32_9G94.pdb --ligand A1D

Scientific warning

CGenFF penalty scores should be reviewed before publication-grade conclusions. Automation reduces typing mistakes, but it does not replace chemical judgment.