VMD-L Mailing List

From: Emma Wu (ewu20_at_illinois.edu)
Date: Wed Oct 07 2020 - 23:20:54 CDT

Thank you so much Daniel! That worked!

Best,
Emma

On Tue, Oct 6, 2020 at 10:51 PM Daniel Fellner <dfel694_at_aucklanduni.ac.nz>
wrote:

> 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
>>
>>
>>