Issues when adding structural water molecules

[OscarDS]

Currently, to add structural water molecules, atom names of water molecules must be OW, HW1 and HW2, and their chain ID must be empty (same ID as the protein chain also works). Hydrogen atoms of water molecules must be present in the pdb file as the current pipeline does not add them.

Details:
Current pipeline does not add H atoms to structural waters, then GROMACS will find: "Fatal error: number of coordinates in coordinate file does not match topology" when trying to execute gmx grompp (BasicInit Step (29/37): grompp).

If water molecules have a different chain ID, e.g. protein as chain A and water as chain W: "Fatal error: Topology include file "protein_Protein_chain_A.itp" not found" at BasicInit Step (29/37): grompp.