Notes on "Parameterization of a new small molecule" (This link)

LigPar Server
ChemInfo Open Babel Server

1. Generate atomistic reference data

On OS X machines, any "mdrun" command needs to add for example "-ntmpi 1"

The force tolerance 'emtol' in the supplied "em.mdp" file will not allow the minimization to complete sufficiently, and thus all other steps will fail. Using the default (which is 10) or 50 works well enough.

Once these two items are fixed, the supplied script will execute without problems. It will take a while!

2. Atom-to-bead mapping

Make sure and use an all-atom PDB file such as a PDB created in Gaussian, or another source such as ChemInfo.

3. Generate the CG mapped trajectory from the atomistic simulation

Please note that the '2_atom-to-bead-mapping' directory is empty; This is in the 'ENAP-in-water' directory. The supplied example files mentioned are in the 'ENAP-worked/…' directory.
Note that on my system, 'python' does not exist; 'python3' used in the '3_map_trajectory_COG.sh' script.

4. Create the initial CG itp and tpr files

Some changes here… make sure the 'system_CG.top' reflects your new molecule/ion.

3_mapped: See note in Step 3 to ensure 'mapped.xtc' is properly created.