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Kenno Vanommeslaeghe

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MacKerell Lab
Computer-Aided Drug Design Center

University of Maryland, Baltimore

20 Penn Street
HSF-II Rm. 631
Baltimore, MD 21201
USA

Division of Acetazolamide into fragments for parametrization

Tutorials

Download the new CGenFF tutorial (tgz archive) that was presented at CECAM's June 2012 and 2013 "Advances in Biomolecular Modelling and Simulations using CHARMM" workshops. This tutorial is fully up-to-date with recent developments, most importantly the availability of the CGenFF program at paramchem.org, and the usage of 3-point scans to determine the force constant for select bonds, angles and improper dihedrals in larger model comounds. It largely skips the details about the target data generation steps and instead focuses more on the details of the actual force field optimization. Special thanks go to Jonathan Chee Yang Loh, whose contributions are marked "jon" in the tutorial files.
Download the accompanying slide show (recommended!) The first part of this presentation is about the (then) state of the art of the CHARMM force field; please skip to slide 76 for the actual tutorial.

Download the old CGenFF tutorial (tgz archive) that was included as supporting information with the CGenFF paper. This tutorial is somewhat outdated, but is still of value because it goes into a little bit more detail concerning the target data generation than the new tutorial.

Note: the CGenFF topology and parameter files included in these tutorials cannot be assumed to be up-to-date! For production calculations, download the latest CGenFF version!

New CGenFF version

Version 4.0 of the CGenFF topology and parameter files (2016-08-16) is integrated in the latest release of the CHARMM additive force field. It is not compatible with the current version (1.0.0) of the CGenFF program at paramchem.org , but version 2.0 of the program is coming soon and will provide compatibility with this version (4.0) of the force field.


Latest CGenFF version

CGenFF logo Notes:

Download version 3.0.1 of the CGenFF topology and parameter files (2015-04-10)

Description: version 3.0.1 is the first release of CGenFF (i.e. CGenFF is no longer beta). It improves upon 2b8 by introducing support for a number of important functional groups and improving support for a number of cyclic moieties. It is compatible with version 1.0.0 of the CGenFF program at paramchem.org .

Changelog (changes from version 2b8 to 3.0.1):


Older CGenFF versions

Note: as CGenFF is still actively growing and being improved, using older CGenFF versions is not recommended for any purpose except reproducing old calculations.

Download version 3.0.0 of the CGenFF topology and parameter files (2015-03-06)

Description: Version 3.0.0 was only distributed to a few privileged parties. From an energetic point of view, it is 100% identical to 3.0.1 . The only differences are:

Changelog

See the change log for version 3.0.1 above.

Download version 2b8 of the CGenFF topology and parameter files (2013-09-04)

Description: version 2b8 is an update of 2b7 that introduces support for a few important functional groups and contains a number of fixes. It is compatible with versions 0.9.7 and 0.9.7.1 beta of the CGenFF program at paramchem.org .

Changelog (changes from version 2b7 to 2b8):

Download version 2b7 of the CGenFF topology and parameter files (2011-10-06)

Description: version 2b7 is a minor update of 2b6 to make the force field compatible with version 0.9.6 beta of the CGenFF program at paramchem.org . Specifically, the introduction of 4 new atom types for 5-membered rings with exocyclic double bonds was required.

Changelog (changes from version 2b6 to 2b7):

Download version 2b6 of the CGenFF topology and parameter files (2010-12-10)

Description: version 2b6 is compatible with versions 0.9.0 and 0.9.1 beta of the CGenFF program at paramchem.org . It was released only on the MacKerell lab's force field page in December 2010.

Changelog (changes from version 2b5 to 2b6):

Download version 2b5 of the CGenFF topology and parameter files (2010-8-13)

Description: version 2b5 was released only on the MacKerell lab's force field page in August 2010.

Changelog (changes from version 2b4 to 2b5):

Download version 2b4 of the CGenFF topology and parameter files (2009-12-31)

Description: version 2b4 was released with CHARMM version 36a4.

Changelog (changes from version 2b1 to 2b4):

Download version 2b1 of the CGenFF topology and parameter files (2009-07-15)

Description: version 2b1 was released only on the MacKerell lab's force field page in July 2009.

Changelog (changes from version 2a5 to 2b1):

Download version 2a5 of the CGenFF topology and parameter files (2009-04-29)

Description: version 2a5 was used for generating the data in the CGenFF paper and the associated (old) tutorial.

Changelog (changes from version 2a0 to 2a5):

Download version 2a0 of the CGenFF topology and parameter files (2008-08-14)

Description: version 2a0 was an early alpha version that was released to a limited audience with CHARMM versions 36a1, 36a2 and 36a3 for the purpose of technical compatibility testing. This version had major issues and is not recommended!!!