A protein–ligand structure can look ready for simulation and still fail during preparation. A common source of trouble is the gap between the ligand as it appears in the structure and the ligand described by its topology: atom names, hydrogens, residue names, or force-field assumptions may not match. Sorting out those details before opening the preparation workflow can save time and make errors easier to diagnose.
This guide focuses on the handoff from ligand parametrization to a prepared, non-covalent protein–ligand system in SAMSON’s GROMACS Wizard. Covalently linked complexes need additional treatment for the linking bond and are outside this workflow.
Start with the force field you plan to use
Choose a ligand parametrization tool that matches the force field you intend to use in GROMACS Wizard. Examples include Antechamber for AMBER, ATB for GROMOS96 54A7, CGenFF for CHARMM, and LigParGen for OPLS-AA. Check the chosen service’s accepted input formats before exporting your ligand from SAMSON.
Before submitting the molecule, check its hydrogens. Many parametrization services require them to be present. In SAMSON, use Edit > Add hydrogens. For ligands in the Chemical Component Dictionary (CCD), SAMSON can use the hydrogen names described there. For other ligands, hydrogen placement is based on valences, so confirm that aromatic rings and charges are already specified. If your ligand file contains this information—for example, a .mol2 file—use it when adding hydrogens.
Keep the structure and topology in agreement
If the ligand is inside a protein–ligand structure, select it in the Document view, then use Home > File > Save selection as… to export it in a format accepted by your parametrization workflow. After parametrization, keep the resulting include topology file (.itp) and, if the service provides one, its updated structure file. Comparing the updated structure with the original helps you spot changes to atom names, hydrogens, or other structural details.
One check is especially important: the ligand name in the structure file must match the name used in the topology data. If the names differ, correct the mismatch before preparing the system. Also check whether the parametrization service supplies a modified force field. Some ligand topologies require one that is not available by default in GROMACS.
Place or update the ligand before preparation
If the complex already contains the same ligand and its structure has not changed, you may be able to keep the existing complex. If parametrization changed the ligand, position the updated ligand at the old ligand’s location and remove the old one. If you are building the complex from separate structures, you can place the ligand with SAMSON’s move tools, dock it with AutoDock Vina Extended, or append it to the protein structure file. When appending, ensure the structures do not overlap and use separate chains or consecutive sequence numbering.
Add the topology in GROMACS Wizard
Open GROMACS Wizard from Home > Apps > Biology > GROMACS Wizard, select the Prepare tab, choose the protein–ligand system in the Document view, and click Set system. In the Choose model section, use Edit for the include topology files and browse to the ligand’s .itp file.
If the topology depends on a custom force field, download it from the parametrization service and add it using the force-field Add button. For example, an ATB-generated topology may come with a corresponding force field such as gromos54a7_atb. Added custom force fields are stored by GROMACS Wizard; the standard force fields are not removed when custom ones are removed.
Finish preparation, then continue the workflow
Complete the remaining preparation choices, including solvent model, periodic boundary box, and ions, using the general preparation guidance. Click Prepare to run the step. If a warning appears, read it rather than treating it as a routine confirmation; the tutorial notes, for example, that a warning may appear when using the ATB GROMOS force field. You can inspect the run log with the Output button.
Once preparation succeeds, the resulting system is saved in the results folder, and you can optionally load it into SAMSON for inspection. The usual next stages are energy minimization, NVT equilibration, NPT equilibration, and production molecular dynamics.
For the full walkthrough, see the SAMSON GROMACS Wizard tutorial for protein–ligand systems.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.