black sheep of the chargePlugin...
Hello - we just run an extensive check of the charge plugin, in an attempt to use it in force field parameterization. There were a bunch of ~30 molecules out of 2200 which caused the chargePlugin to throw a NullPointer. We use resonant forms for charge calculations and explicitly enter the major microspecies as plugin input. The whole happens with an piece of code (Conformers.java) attempting to prepare organic molecules for our own conformational sampler, e;g. assign charges, force field types and create at least ONE starting geometry, but we know that, at least for some out of the no_charges.smi, a plain use of chargePlugin in whatever context also leads to the (same?) NullPointer.
Actually, we know more by now: problems stemmed from setting TakeResonantStructures to true. We added a catch which, if calculation fails with resonant structures, will attempt one without - and succeed in all the previously listed cases. Unfortunately, we're skeptical about ignoring resonant structures - try, for example, guanidine: without resonance, the positive charge will stick to a single N out of the 3 equivalent!
Thanks for reporting this bug. It have been fixed.
Thank You for fixing the error. Can we get the new version?
I've been looking for it at the "Download JChem test releases" page, but the latest file is still jchemTEST_2006_08_25.tar.gz - the version we use now.
It will be included in the JChem 3.2 version (coming soon).