WARNING: this is an archive page that mostly reflects my research activities at the University of Maryland, Baltimore up to the end of 2015.
A notable exception is my CGenFF section, which is hosted on this site (mackerell.umaryland.edu) for the time being.
Click here for my (somewhat) updated home page at my current institution.
University of Maryland, Baltimore
CHARMM versions 36 and higher support CGenFF by default. Version 35 should be compiled with the optional preflx keyword "CGENFF". There is also a patch to add CGenFF support to the CHARMM 34b2 source. If you're planning to compile any CHARMM version older than 36 with CGenFF support, be sure to check out the FAQ!
The early alpha version of CGenFF that was distributed with c36a had some issues and is now obsolete. Only use the version from this website!
When writing a paper using CGenFF parameters, it should be mentioned which version of the CGenFF force field and which version of the CGenFF program (if applicable) was used, otherwise the results are not reproducible!
Never use CGenFF for biological macromolecules. The Protein, Nucleic Acid, Carbohydrate and Lipid force fields are highly optimized for their specific purpose. The general force field is designed to cover any combination of chemical groups. This inevitably comes with a decrease in accuracy for representing any particular subclass of molecules, such as proteins, nucleic acids, carbohydrates and lipids. It is for this reason that we removed the amino acids, nucleotides,... from CGenFF. Here is what you should do in order to represent a typical protein-ligand system:
read rtf card name @TOPPAR/top_all36_prot.rtf read param card flex name @TOPPAR/par_all36_prot.prm read rtf card append name @TOPPAR/top_all36_cgenff.rtf read para card flex append name @TOPPAR/par_all36_cgenff.prm stream toppar_water_ions.str