Running OpenMMDL Setup

This page displays the preparation paths and forcefields available in OpenMMDL and showcases the application of OpenMMDL Setup.

To start the OpenMMDL Setup we need to activate the openmmdl environment. To do this we have to enter the following command lines:

conda activate openmmdl

Now that we have activated the openmmdl environment we can start OpenMMDL Setup. To do this you need to type the following:

openmmdl setup

This will open the OpenMMDL Setup, which you can use for the creation of the input files for OpenMMDL Simulation.

There are two possible options to create the input files for OpenMMDL Simulation:

1. The PDBFixer path, where a pdb file of the protein is used as an input for the preparation and simulation. The tutorial for the PDBFixer path can be found here.

Here is the table of the currently available forcefields and water models for the PDBFixer path:

PDBFixer path AMBER forcefields

Water model	AMBER14 / AMBER19	AMBER99SB / AMBER99SB-ILDN / AMBER03 / AMBER10
TIP3P	✓	✓
TIP3P-FB	✓	✓
SPC/E	✓	✓
TIP4P-Ew	✓	✓
TIP4P-FB	✓	—
TIP5P	—	✓
OPC3	✓	✓
OPC	✓	✓

PDBFixer path CHARMM forcefields

Water model	CHARMM36	CHARMM36 2024
SPC/E	✓	✓
TIP4P-Ew	✓	✓
TIP5P	✓	✓
CHARMM default	✓	✓
TIP3P-PME-B	✓	✓
TIP3P-PME-F	✓	✓
TIP4P-2005	✓	✓
TIP5P-Ew	✓	✓

2. The Amber path, where prmtop and inpcrd files are used the preparation and simulation. This path allows us to either use already prepared prmtop and inpcrd as an input or create the prmtop and inpcrd from PDB files of the receptor and ligand. The tutorial for the Amber path can be found here.

In the table, the first row is the default setting, and the term other allows users to type their desired forcefields from those accessible in AmberTools 22.0 into the designated textbox.

Glycoprotein receptors (Amber path)

The Amber path additionally offers a Glycoprotein receptor type for proteins with covalently attached N- or O-linked glycans. When selected, OpenMMDL Setup:

1. Detects sugar residues by PDB residue name (NAG, NDG, BMA, MAN, FUC, FUL) and finds glycosidic linkages from CONECT records (falling back to a distance scan if absent).

2. Renames residues and atoms to GLYCAM-06j-1 conventions (e.g. NAG → 0YB / 4YB, MAN → 0MA / 3MA / 6MA, with the trimannose branch point as VMB).

3. Emits explicit bond statements for every protein-glycan and glycan-glycan covalent link, injected into the generated tleap.in after loadpdb.

4. Sources both the chosen protein force field (e.g. leaprc.protein.ff14SB) and the glycan force field (leaprc.GLYCAM_06j-1 by default).

Only the common N-glycan core sugars listed above are currently supported. Unrecognised PDB sugar codes or non-canonical linkage patterns raise a descriptive error; see openmmdl/openmmdl_setup/glycoprotein.py for the verified GLYCAM tables.