issues with QMMM and parameters

From: Francesco Pietra (
Date: Wed Jul 15 2020 - 02:23:43 CDT

I am bringing again to the attention the occurrence of scattered issues
with "simple" QMMM. That is, while MD always runs without problems, a
slight change in the molecular structures dealt with can lead to QMMM being
unable to find parameters.

Previously I noticed, and brought to the attention in this forum, this
problem with the complex of a nucleosides and small organic molecules in
TIP3 water. A slight change in the structure of the small organic molecule
made QMMM unable to find parameters. Now I am faced by this problem with a
small organic molecule and dioxygen in methanol as solvent, in the absence
of any biopolymer, where, again, MD has no problems in running without or
with distance colvars.

I wonder whether similar issues have ever been encountered elsewhere

francesco pietra

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