When the system contains a non-standard small molecule, such as a protein-bound ligand, a few extra steps are necessary. The grand.utils.write_conect() function write CONECT lines to a PDB file for the ligand bonds, which is necessary for OpenMM to understand the ligand topology from a PDB structure. Additionally, an XML file for the ligand parameters should be written using the grand.utils.create_ligand_xml() function. These functions could be run prior to the simulation script if desired.
The documentation for these functions can be found in the "grand package" section.
../../examples/scytalone/scytalone.py