We applied a major update to the CGenFF program - the new beta version is 0.9.6 . The output of this new version should only be used with the new 2b7 release of the CHARMM General Force Field
. Version 0.9.6 of the CGenFF program features the following improvements:
- Improved parameters and penalties for substituted planar rings and conjugated double bonds
- "Guess bond orders from connectivity" feature
- Improved atom typing of polyaromatic heterocycles
- Improved accuracy for ketals, neutral enamines and beta-substituted enals
It is strongly recommended to read the detailed description of these improvements below (also available on the changelog page
). If you cannot do so right now, at least note the following caveats:
Detailed description of the improvements in 0.9.6More accurate parameters and penalties for substituted planar rings and conjugated double bonds
- Using the new "Guess bond orders from connectivity" feature is risky and should be avoided whenever possible
- Resubmitting existing molecules to the new version will often give rise to higher penalties. This does not imply that the new parameters are less accurate; rather, it means that the old penalties were too low.
After months of beta testing, it was discovered that in some cases, molecules with substituted planar rings or conjugated double bonds yielded unreasonable parameters with misleadingly low penalties. This turned out to be a fundamental shortcoming in the parameter assignment algorithm, necessitating the implementation of substantial new functionality, which is now available in version 0.9.6. The problem was especially pronounced for angle parameters in substituted planar 3- and 5-membered rings. If you have encountered incorrect behavior in such molecules, or molecules with conjugated double bonds, it is advisable to submit the affected compounds to our new version, and contact us if the problem persists or if anything else is odd. Remember that our software is still in beta stage, and its quality depends on your feedback!
That said, note that the new version will often give you different parameters with substantially higher penalties. This is normal and does not imply that the old parameters were more accurate; on the contrary, it means that the penalties for these parameters were too low in the old version, and that after adjusting them upwards, better (ie. lower-penalty) parameters turned out to be available."Guess bond orders from connectivity" feature
It has been brought to our attention that some popular free molecular editors (most noteworthy VMD) produce mol2 files with invalid bond orders
. Also, distorted pdb files are frequently submitted, causing OpenBabel to guess the bond orders incorrectly. To work around these problems, the new version of the interface features a check box to instruct the program to discard input bond orders and guess the bond orders from the connectivity. We would like to stress that this feature should be used with EXTREME CAUTION! Ordinarily, the program checks whether the input bond orders are consistent with the connectivity, and returns an error if this is not the case. Doing so has already caught many problems that would otherwise lead to incorrect parameters. However, this check is disabled by choosing "guess bond orders..." This implies that if, for instance, hydrogen atoms are missing or placed incorrectly, the program may output grossly inaccurate parameters without warning. Additionally, guessing bond orders may not always work on 3rd-row and heavier elements.Improved atom typing of polyaromatic heterocycles
In some cases, polyaromatic heterocycles containing positive nitrogen atoms and/or carbonyl groups received incorrect atom types. This bug is fixed in version 0.9.6.Improved accuracy for ketals, neutral enamines and beta-substituted enals
This is the result of our ongoing extension of the CHARMM General Force field.