News & Events
  • CGenFF out of beta: version 1.0.0 - April 17, 2015
  • Version 1.0.0 of the CGenFF program was made available through the ParamChem website. The output of this new version should only be used with the new 3.0.1 release of the CHARMM General Force Field. With these new versions, the CGenFF program and force field are officially out of beta; very few bugs popped up during the last year and we now support a sufficiently large majority of drug-like molecules for routine use in Computer-Aided Drug Design projects. This also implies that we're open to providing machine-friendly access to nonprofit collaborators; please contact us if you are interested. For-profit users may obtain the CGenFF program from SilcsBio, LLC.
  • Version 1.0.0 of the CGenFF program improves upon 0.9.7.1 by introducing support for a number of important functional groups and improving support for a number of moieties. Here is a full list of improvements:
    • Introduced support for "bipyrrole-type" sp2-sp2 single bonds between 5-membered rings
    • Fixed bug where in rare cases, atoms were incorrectly recognized as "bipyrrole-type"
    • Introduced support for "bipyridine-type" nitrogen-containing single bonds between 6-membered aromatic rings
    • Greatly improved nonbonded representation of terminal alkynes
    • New support for bicarbonates/hemicarbonates, sulfamate anions, sulfamides and isocyanates
    • Improved support for semi-flexible 5-membered rings and gamma-lactones, non-amide carbonyls in 6-membered aromatic rings, heteroaromatic bicycles and biphenyls, thioether substitutions on heterocycles, taurine amides, N-benzylamides, 1-alkyl-1,2,3-triazoles and phosphoramidates
    • Improved support for neutral sulfamates
    • Substantial improvements in charges on aromatic heterocycles
    • Reduced numerical noise in charge assignment
  • It is recommended that users read the detailed description of these improvements in the Change Log.
  • Server migration + Utilities + CGenFF version 0.9.7.1 - March 14, 2014
  • The CGenFF program was migrated to a new server: cgenff.paramchem.org . Simultaneously, AGPL-licensed utilities to use the CGenFF output with GROMACS and with the DOMDEC and implicit solvent features in CHARMM were released on our new utilities page. Finally, the opportunity was used to make version 0.9.7.1 of the CGenFF program available. Just like 0.9.7, the output of this new version should only be used with the new 2b8 release of the CHARMM General Force Field. The following improvements were made:
    • Fixed atom typing bug in 5-membered ring lactones
    • Explicit warning message for fullerene-like structures
    • Explicit warning messages for sulfuric and sulfonic acids and bisulfate anions
    • Explicit warning message for amidinium resonance in 6-membered aromatic ring
    • Reject molecules with unsupported bipyridine-type inter-aromatic bond
    • Reject molecules with unsupported bipyrrole-type carbons and nitrogens
  • Just like with the previous release, it is recommended that users read the detailed description of these improvements in the Change Log. In particular, if you are currently using CGenFF-generated 5-membered ring lactone parameters in an active project, it might be a good idea to assess the impact of the atom typing bug. Just like in the previous release, only a minute percentage of molecules are affected by the bugs that are now fixed.
  • CGenFF version 0.9.7 - September 4, 2013
  • Version 0.9.7 of the CGenFF program was made available through the ParamChem website. 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 got rid of almost all 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 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 Change Log. In particular, if you are currently using CGenFF-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; less than 1 in 1000 molecules are seriously affected by the bugs that are now fixed.
  • CGenFF version 0.9.6 - October 6, 2011
  • Version 0.9.6 of the CGenFF program was made available through the ParamChem website. The output of this new version should only be used with the new 2b7 release of the CHARMM General Force Field. Version 0.9.6 of the CGenFF program features the following improvements:
    • Improved parameters and penalties for substituted planar rings and conjugated double bonds
    • "Guess bond orders from connectivity" feature
    • Improved atom typing of polyaromatic heterocycles
    • Improved accuracy for ketals, neutral enamines and beta-substituted enals
  • It is strongly recommended that users read the detailed description of these improvements in the
    Change Log. If you cannot do so right now, at least note the following caveats:
    • Using the "Guess bond orders from connectivity" feature is risky and should be avoided whenever possible
    • Resubmitting existing molecules to the new version will often give rise to higher penalties. This does not imply that the new parameters are less accurate; rather, it means that the old penalties were too low.
  • Biophysical Society's 55th Annual Meeting - March 5-9, 2011
  • Alex MacKerell and Kenno Vanommeslaeghe attended the Biophysical Society's 55th Annual Meeting in Baltimore, MD. Kenno Vanommeslaeghe presented a poster on the CGenFF program and the ParamChem project. From 30 minutes before the start of the poster session until 15 minutes past the end, this poster was continuously attended by multiple current and future CGenFF users discussing the workings of the CGenFF program.
  • CGenFF version 0.9.1 - January 25, 2010
  • Version 0.9.1 of the CGenFF program was made available through the ParamChem website. This version has improved functionality for renumbering atoms with duplicate names; the renumbering algorithm in version 0.9.0 in rare cases behaved incorrectly. It also has some minor improvements in the warning and error messages and in the treatment of spiro compounds. Just like version 0.9.0, version 0.9.1 of the CGenFF program requires version 2b6 of the CGenFF Force Field.
  • Official launch of CGenFF program version 0.9.0 beta - December 20, 2010
  • In the first stage of the roll-out of the ParamChem engine, the CGenFF program for automatic atom typing and assignment of parameters and charges by analogy was revealed to the public. This functionality can be used in a standalone fashion for rapid prototyping of parameter sets for organic molecules, and in the bigger picture of force field parameterization, it is a good initial guess generator.
  • XXIst International Symposium on Medicinal Chemistry - September 5-9, 2010
  • At the XXIst International Symposium on Medicinal Chemistry in Brussels, Belgium, Kenno Vanommeslaeghe presented a poster on the CGenFF program and the ParamChem project, drawing considerable interest from computational medicinal chemists.