We released another update - the new beta version is 0.9.7 . The output of this new version should only be used with the new 2b8 release of the CHARMM General Force Field. Version 0.9.7 of the CGenFF program is mainly a "monster bugfix release", in which we corrected almost all of the user-reported and self-discovered issues that accumulated over the last 2 years of beta testing. Additionally, we added support for a few important functional groups. Here is a full list of improvements:
  • New support for saturated 4-membered rings
  • Improved support for epoxides, aliphatic nitro groups, neutral organic sulfonates, sulfamates, benzoic acid esters and derivatives
  • Better charge (and parameter) assignment on positive amines
  • Residue IDs (RESI) now truncated at 6 characters for improved compatibility
  • Fixed penalty score for ranking resonance structures
  • Better guessing of bond orders of sulphur and phosphorus-containing moieties
  • Better aromaticity perception on some sulfur-containing rings
  • More sophisticated aromaticity perception algorithm
  • Improved parameter assignment on systems with more than 2 conjugated aliphatic rings
  • Correct atom typing when given incorrect bond orders on nitro groups, negative carmabates
  • Corrected atom typing on sulfoximines, phosphorimidates, sulfenates
  • Fixed formal charge on positively charged bridging nitrogens conjugated to another nitrogen
  • Maximum number of atoms increased to 384
  • Fixed atom renumbering
  • "Penalty" is now uppercase when including parameters that are already in CGenFF
  • Clearer warning messages about sulfinamide and sulfurous diamide not being explicitly supported
  • Tweaked warning and error messages for nitrates
  • Miscellaneous tweaks in assignment of charges and parameters by analogy
It is recommended that users read the detailed description of these improvements in the changelog. In particular, if you are currently using paramchem-generated molecules in an active project, it might be a good idea to check whether your molecule gets the same atom types and total charge in the new beta version. That said, there is no reason to panic; we estimate that less than 1 in 1000 molecules are seriously affected by the bugs that are now fixed.