VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Sun Jul 14 2024 - 12:19:46 CDT

* also the original .inp water position is also bound to the adjacent
C-atom at an even closer distance than C5 which should not be
i.e. flipping the water would eliminate this error.

On Fri, Jul 12, 2024 at 1:58 PM Joel Subach <mjsubach_at_alumni.ncsu.edu>
wrote:

> Hello VMD Community, I hope you're well:).
>
> Towards the above-topic, my Acceptor Ligand C5 ffTK Water Int Tab
> generated .inp File exhibits water coordinates that need to be flipped to
> the other side of the ligand C5´s interaction-site.
>
> The current distance of the ffTK generated .inp water-C5 interaction is a
> satisfactory 2.0 A (see inp screenshot attached), however, the final ORCA
> generated .xyz water-C5 coordinates exhibit this waters interaction with an
> adjacent C-atom resulting in a water-C5 distance of 5.0 A (see xyz
> screenshot attached).
>
> Flipping this water to the other side should fix this issue and how many
> of these errors may I discard altogether to be insignificant (my ligand is
> 66-atoms)?
>
> Thanks if you know:),
> Joel 🚀
>