VMD-L Mailing List

From: Emma Wu (ewu20_at_illinois.edu)
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 (
https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/29293.html) 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!

Best,
Emma