These files would be easier to view if they had been attached (or referenced) as .txt files, as outlined in the READ BEFORE POSTING topic.

The high penalties do not mean the parameters are bad, just that the five membered ring topology is not well represented in the database.

This would appear to be a planar fused ring aromatic system, so I would run some gas phase low friction Langevin simulations of the new molecule, and a few similar molecules already in the CGenFF topology file, such as pyrimidines and other fused ring aromatic molecules. Then, align the trajectory coordinates using the ring heavy atoms, compute the average coordinates, and finally compute the fluctuations about the average. If the ring atom fluctuations are comparable to those from existing known planar molecules, that would be reasonable first pass test.


Rick Venable
computational chemist