I was performing an energy minimization using GAFF on a simple methacrylic acid molecule when I noticed something very strange: The carbonyl oxygen of the carboxylic acid group swallowed the acidic hydrogen and formed a three membered ring (CO2).
This strikes me as extremely strange since GAFF is not a reactive (QM) forcefield and this has never happened before (with previous versions) (now running 1.0.3 on Mac OS X). Has this happened to anyone else? Is there an explanation for this behavior?
Doing some further investigations, the carboxylic acid group seems to present this problem for multiple molecules when performing an energy minimization using GAFF. Benzoic acid does not display this behavior though multiple other smaller acids does.
Any ideas as tho why this is occurring?