CGenFF main page

CGenFF

This page was originally developed by Kenno Vanommeslaeghe here.

MacKerell Lab
Computer-Aided Drug Design Center

University of Maryland, Baltimore
Baltimore, MD 21201
USA

Welcome to the CHARMM General Force Field for organic molecules. If you want to perform simulations on a system that contains a small organic molecule using the CHARMM force field, you've come to the right place. The CGenFF program will provide you with parameters for your specific molecule, which you can read into your simulation software together with the main CGenFF topology and parameter files and parts or all of the CHARMM36 biomolecular force field. Before starting the simulation, please take a moment to examine the penalty scores in the output of the CGenFF program. If they are large, chances are that you'll need to re-optimize the parameters. How to do so is described in K. Vanommeslaeghe et al., J. Comput. Chem. 2010, 31, 671-690 and illustrated by means of two tutorials that can be downloaded from the download page. The procedure is made easier by the lsfitpar program for robust fitting of bonded parameters. Below are some more links and notes.

Usage information for the CGenFF program for automatic atom typing and assignment of parameters and charges by analogy

[K. Vanommeslaeghe et al., J. Chem. Inf. Model. 2012, 52, 3144-3154; K. Vanommeslaeghe et al., J. Chem. Inf. Model. 2012, 52, 3155-3168]

Frequently Asked questions

Download page (includes the CGenFF tutorials)

Important notes - read this before using CGenFF:

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:
1. With the latest CHARMM force field release, you can just read in the topology and parameter files as follows:
```
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
```
2. (optional) read in your own stream file:
```
stream my_ligands.str
```
Note: the latest CGenFF version is often ahead of the CHARMM force field release.
Check out the FAQ!

This material is based upon work supported by the National Science Foundation under Grant No. 0823198. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Last updated Sunday, the 31st of May 2015