Just a quick update : converting the Desmond CMS to Gromacs top/gro using InterMol as mentioned above and then making use of the OpenMM's GromacasTopologyFile works okay. Its roundabout, but works. I am validating energies just to be doubly-sure but if simulation trajectories are to go by, this hold...

Thank you Emilio. Motivation to work with Desmond comes from its capability of supplying ligand topology and parameters. Thank you for the note on the limitations of the DMS. That makes it less attractive. Although this may seem a circuitous way, I am exploring converting the cms first into gromacs ...

I am trying to read in a Desmond cms file to run an MD simulation in OpenMM. I could only find this class : DesmondDMSFile. But when I try to read in CMS file using this class constructor, I bump into the following error : sqlite3.DatabaseError: file is encrypted or is not a database Since, CMS is a...