News & Events
  • Current Status & Future Developments
  • The ParamChem project has run out of funding before an automatic graphical user interface for parameter optimization could be released. However, the technologies developed as part of the project represent substantial advancements in the field; please visit our technology page to access the CGenFF program, the lsfitpar parameter fitting software etc.
    In parallel, K. Vanommeslaeghe and the MacKerell lab remain strongly committed to keep on improving ParamChem's core CGenFF functionality. Some of the ongoing and planned projects are:
    • Continuing expansion of CGenFF in the width (more chemical groups) and depth (better accuracy)
    • More "simulation-friendly" output in different formats; tight integration of the GROMACS conversion script and other utilities into the web interface
    • A machine-friendly interface to the CGenFF service
    • A unified "CHARMM program" that accepts a complete simulation system and automatically chooses the right part of the force field for the right part of the system (protein FF for proteins, carbohydrate FF for sugars, CGenFF for non-biomolecules,...)
    • Support for structures with large-scale resonances
    • Better charge assignment
    • Improvement of electrostatic treatment through introduction of lone pair particles
    • A polarizable CHARMM General Force Field
  • News Archive
  •   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 ParamChem-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 interface. 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 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; less than 1 in 1000 molecules are seriously affected by the bugs that are now fixed.
  •    "Novice interface" development workshop - March 5-16, 2012
  • Following difficulties in predicting a time frame for solving the continued stability and cross-platform compatibility issues in the fully-featured ParamCAD "expert interface", it was decided to first prepare the Jamberoo-based "novice interface" for release. As the latter was in a very early stage of development, a workshop was held in Baltimore, MD from the 5th till the 16th of March in order to develop a dihedral fitting interface that is intuitive to the novice user yet scientifically useful.
  •   6th ParamChem meeting - October 30 - November 2, 2011
  • The 6th ParamChem meeting took place in Lexington, KY between the 30th of October and the 2nd of November, 2011. Major points of discussion in this meeting were the GUI/molecular editor and the "vertical integration" of all components of the ParamChem software stack, namely the GUI, the CGenFF service at paramchem.org, the XBaya workflow software, the middleware services, the back-end scripts and the back-end binaries. In order to facilitate testing the resulting integrated software stack from a user's perspective, it was agreed to polish the dihedral optimization functionality of the ParamCAD GUI to a level of quality suitable for alpha testing.
  •   CGenFF version 0.9.6 - October 6, 2011
  • Version 0.9.6 of the CGenFF program was made available through the ParamChem interface. 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.
  •   5th ParamChem meeting - April 27-30, 2011
  • The 5th ParamChem meeting took place at NSCA from the 27th of April till the 30th of April, 2011. The main goal of this meeting was to bring together progress made in the different participating labs into an integrated functionality that can be exposed to the user, starting with the optimization of dihedral parameters from initial guesses. Integration of the molecular editor with authentication infrastructure, the initial guess generator and back-end optimization algorithms was discussed. A working workflow for dihedral optimization, including generation of target data and automatic parameter optimization was constructed.
  •   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 ParamChem users discussing the workings of the ParamChem engine.
  •   CGenFF version 0.9.1 - January 25, 2010
  • Version 0.9.1 of the CGenFF program was made available through the ParamChem interface. 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 - 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 will fulfill the role of 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.
  •   240th ACS National Meeting & Exposition - August 22-26, 2010
  • The 240th ACS National Meeting & Exposition took place in Boston, MA. Jayeeta Ghosh was one of the invited speakers for the "Computer Modeling: the Wave of the Future" session, in which she informally mentioned ParamChem's work on parameterization, resulting in very positive feedback from the audience. She shared ParamChem's vision with other presenters and audience during other sessions. In another talk, she presented her work on skin lipid membrane and penetration modifier.
  •   4th ParamChem meeting - July 28-30, 2010
  • The 4th ParamChem meeting took place in Lexington, KY between the 28th of July and the 30th of July, 2010. This meeting focused predominantly on principles and practical aspects of the parameterization workflow. Other aspects of the ParamChem project such as the molecular editor and the CGenFF program and were also discussed, and checkpoints were set for a smooth assimilation of the different components of the project.
  •   239th ACS National Meeting & Exposition - March 21-25, 2010
  • Team members presented the ParamChem project at the ACS meeting in San Francisco, CA.
  •   3rd  ParamChem meeting - October 14-16, 2009
  • The third ParamChem meeting took place in Baltimore, MD. The agenda focused on global directions and checkpoints of the project, parameter optimization, middleware and back-end functionality, and also included discussion about the User Interface and Database system.
  •   238th ACS National Meeting & Exposition - August 16-20, 2009
  • Kenno Vanommeslaeghe participated in the ACS meeting held in Washington, DC. In his presentation, he articulated the progress of the ParamChem project. He also pointed out the developements made to the front end interface, the workflow and the back end infrastructure.
  •   2nd ParamChem meeting - June 25-26, 2009
  • ParamChem's second meeting was held in Washington, DC. John Connolly, Vikram Gazula, Michael Sheetz from CCS, UKY and Kenno Vanommeslaeghe from UMB and Sudhakar Pamidighantam from NCSA attended the meeting. The status of the Workflow, Database, Molecular Editor, etc. were discussed. Checkpoints were set aiming at setting up prototype infrastructure for automated parameter optimization.
  •   NanoCAD HIG ready - April 27, 2009
  • New internal Human Interface Guidelines for the NanoCAD molecular editor were finalized.
  •   Xbaya integrated with GridChem - April 17, 2009
  • Xbaya was successfully integrated with GridChem. This development facilitates workflow management in the ParamChem project.
  •   Xbaya integrated with molecular editors - March 16, 2009
  • Initial integration of Xbaya and molecular editors ANU, JavaEditor, GDIS, JMOL was completed.
  •   1st ParamChem meeting - February 24-27, 2009
  • The first ParamChem meeting took place at NCSA between Sudhakar Pamidighantam, Michael Sheetz and Kenno Vanommeslaeghe. Several aspects of the project including the cyber infrastructure's architecture and the workflow were discussed. Time line schedules were constructed for piecewise development and integration of modules during the first phase. Periodic discussion / meetings were also agreed upon in order to coordinate the project and communicate recent developments.