mm-parm

Overview

Summary: Build Amber prmtop/rst7 topology files from a PDB with automatic GAFF2 ligand parameterization, disulfide detection, and optional hydrogen addition via PDBFixer.

mlmm mm-parm generates Amber topology/coordinate files from a PDB. The input PDB is used without structural fixing by default. Unknown residues are automatically parameterized with antechamber (GAFF2, AM1-BCC charges) and parmchk2. Residues explicitly listed in --ligand-charge are treated as ligand/cofactor definitions and are prioritized for GAFF2 parameterization. Disulfide bonds are inferred geometrically from SG-SG (or S-S) distances within 2.3 Å. Amino-acid residues listed in AMINO_ACIDS but still unrecognized by the selected force field are not handled automatically – the build aborts with a message asking you to parameterize them manually.

When --add-h, hydrogens are added at the specified --ph using PDBFixer before tleap processing. No other structural fixing is performed. With --ff-set ff14SB, the force field switches to ff14SB (proteins) + TIP3P (water) (+ phosaa14SB).

Minimal example

mlmm mm-parm -i input.pdb --out-prefix complex \
 -l "GPP=-3,MMT=-1" --ligand-mult "GPP=1,MMT=1"

Output checklist

  • <prefix>.parm7 – Amber prmtop topology

  • <prefix>.rst7 – Amber ASCII inpcrd coordinates

  • <prefix>.pdb – LEaP savepdb output (see naming rules below)

Common examples

  1. Basic topology build with hydrogen addition.

mlmm mm-parm -i input.pdb --out-prefix complex \
 -l "GPP=-3,MMT=-1" --ligand-mult "GPP=1,MMT=1" \
 --add-ter --ff-set ff19SB --add-h --ph 7.0

  1. Build without hydrogen addition.

mlmm mm-parm -i input.pdb --out-prefix complex \
 -l "GPP=-3" --no-add-h

Workflow

  1. Input preparation – The input PDB is read as-is (no structural fixing). If --add-h is set, hydrogens are added via PDBFixer at the specified --ph.

  2. TER insertion – When --add-ter (default), TER records are inserted before and after contiguous blocks of ligand/water/ion residues.

  3. Unknown residue parameterization – Residues not recognized by the force field are parameterized with antechamber (GAFF2, AM1-BCC) and parmchk2. Residues named in --ligand-charge are prioritized for this route. Formal charge and spin multiplicity are controlled via --ligand-charge and --ligand-mult.

  4. Disulfide detection – CYS/CYM/CYX pairs with SG-SG (or S-S) distance <= 2.3 Å are bonded automatically.

  5. Topology build – tleap generates parm7/rst7/pdb files using the selected force field set.

CLI options

Option

Description

Default

-i, --input PATH

Input PDB (used as-is unless --add-h).

Required

--out-prefix TEXT

Output prefix for parm7/rst7/pdb files.

Stem of input PDB

-l, --ligand-charge TEXT

Map residue name to formal charge, e.g. "GPP=-3,MMT=-1".

None

--ligand-mult TEXT

Map residue name to spin multiplicity, e.g. "HEM=1,NO=2". Unspecified residues default to singlet (1).

None

--keep-temp/--no-keep-temp

Keep intermediate files/logs in a working directory (for debugging).

False

--add-ter/--no-add-ter

Insert TER before/after ligand/water/ion blocks.

True

--add-h/--no-add-h

Add hydrogens at --ph using PDBFixer.

False

--ph FLOAT

pH for PDBFixer hydrogen addition (used only with --add-h).

7.0

--ff-set {ff19SB|ff14SB}

Force field set: ff19SB (default) or ff14SB.

ff19SB

See Also

  • Common Error Recipes – Symptom-first failure routing

  • Troubleshooting – Detailed troubleshooting guide

  • all – End-to-end workflow (calls mm-parm internally)

  • extract – Extract active-site pocket before parameterization

  • define-layer – Define ML/MM layers after building topology