VMD-L Mailing List

From: Daniel Fellner (dfel694_at_aucklanduni.ac.nz)
Date: Tue Oct 06 2020 - 22:51:15 CDT

You should flip the GAU input for the water interaction which is
experiencing steric clashes:

e.g. if the C6 water clashes with the carbonyl along its Z-matrix, flip the
C6 water by adding or subtracting 180 deg from the first dihedral in the Z
matrix list

*Daniel Fellner BSc(Hons)*
PhD Candidate
School of Chemical Sciences
University of Auckland
Ph +64211605326

On Wed, Oct 7, 2020 at 4:18 PM Emma Wu <ewu20_at_illinois.edu> wrote:

> 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
>
>
>