Summary of output data and its utilization
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 HERE. 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