The output is a CHARMM-compatible "stream file", which can be read by compatible molecular simulation programs such as CHARMM,
NAMD, GROMACS,... after reading the CHARMM General Force Field (CGenFF). This force field, along with a basic example showing how to
apply it together with a CGenFF-generated stream file, can be found
CHARMM stream files are human-readable plain-text files; it is strongly recommended to "manually" examine the stream file
prior to running simulations. If warnings are present, the parameters may not be sufficiently accurate for use. The stream file
also contains "penalty scores" associated with the partial charges and parameters. Penalties between 10 and 50 indicate that some
basic validation is recommended; penalties higher than 50 usually are usually associated with parameters or charges that need additional
optimization. It should be noted that even in cases were the penalty score is low, the accuracy of the parameters cannot be guaranteed.
In all cases it is recommended that the user perform some level of validation of the parameters prior to use.
Both CGenFF and the functionality exposed through this interface ("the CGenFF program") are in beta stage of development.
Although extensive testing has been performed during the alpha stage, we are not responsible for potential issues.
The CGenFF force field and program will be updated in tandem at regular dates. These updates will increase the number of supported
chemical groups, but may also lead to small changes in the charges and parameters assigned to a given molecule. Therefore, when citing
CGenFF, it is important to include the version number of the interface (currently 1.0.0) and the force field (currently 3.0.1).
Cite CGenFF respectively as
- K. Vanommeslaeghe, E. Hatcher, C. Acharya, S. Kundu, S. Zhong, J. Shim, E. Darian, O. Guvench, P. Lopes, I. Vorobyov, A. D. MacKerell Jr., CHARMM General Force Field: A Force field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Field, J. Comput. Chem. 2010, 31, 671-690.
- W. Yu, X. He, K. Vanommeslaeghe, A. D. MacKerell Jr., Extension of the CHARMM General Force Field to Sulfonyl-Containing Compounds and Its Utility in Biomolecular Simulations, J. Comput. Chem. 2012, 33, 2451-2468.
- Atom typing and assignment of parameters and charges by analogy:
- K. Vanommeslaeghe, A. D. MacKerell Jr., Automation of the CHARMM General Force Field (CGenFF) I:
bond perception and atom typing, J. Chem. Inf. Model. 2012, 52, 3144-3154.
- K. Vanommeslaeghe, E. P. Raman, A. D. MacKerell Jr., Automation of the CHARMM General Force Field (CGenFF) II: Assignment of bonded parameters and partial atomic charges, J. Chem. Inf. Model. 2012, 52, 3155-3168.
- CGenFF interface at paramchem.org: https://cgenff.paramchem.org