From: Emma Wu (
Date: Tue Oct 06 2020 - 22:13:31 CDT

I am pretty new to parameterization and I am currently trying to
parameterize a molecule using fftk but I am stuck on the water interactions
tab. I noticed that there are some steric clashes between interaction sites
of a planar C6 ring and a nearby carbonyl. I was reading through previous
answers/questions on the mailing list and I came across ( a post
that seems to have an answer that might help me. Basically they mentioned a
quick fix was to "manually edit the Z matrix of the GAU input to flip the
water molecule to the other side of the ring" but I am confused on this
statement. Should I be flipping the GAU input for the ring or for the
carbonyl that are sterically clashing in my case? If so, why? Thank you so
much for any suggestions and inputs!