From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Tue Nov 05 2024 - 03:28:07 CST

* Maybe an Orca charge adjustment of 0 is needed to modify steric clashes
and or an unfavorable environment, any insight would be appreciated,
thanks:)

On Tue, Nov 5, 2024 at 12:39 AM Joel Subach <mjsubach_at_alumni.ncsu.edu>
wrote:

> Hello VMD Forum,
>
> towards the above topic, I am running the Orca Command:
>
> (base) Joels-MacBook-Air:14C-DON-C8i joelsubach$ orca 14C-DON-C8i.inp >
> 14C-DON-C8i.output.out
> (in this case DON means donor)
>
> to generate the above output.out file which will be subsequently used
> towards a VMD ffTK Charge Optimization.
>
> The above C8i .inp File exhibits a -2 Charge via its two
> negatively-charged carboxylate ion COO- groups generated via an Avogadro pH
> of 7.4
> (prior the ligand exhibited instead two carboxyl group COOH groups (see
> screenshot attached via Dropbox Link below, figure labeled Charge-2.)
>
> I had successfully executed the above command for several other .inp files
> within this structure with this -2 charge within the respective
> .inp files, however, this C8i.inp file seems to be generating a fly-away
> at this proper -2 charge but when I change the C8i.inp file to a
> 0-charge (C8.inp) the orca command successfully generates the proper water
> optimization distance (see screenshots C8i_FlyAway and C8 respectively also
> within below Dropbox Link).
>
> Accordingly my inquiry, may I in this instance use the 0-charged .inp file
> exhibiting the proper water displacement out.out file or
> must I resolve this issue within the structure i.e. the ffTK Manual states:
>
> `Cases in which water molecules appear to settle at large distances or
> even “fly away”, indicate the absence of the expected minimum for the given
> interaction site. This can be due to improperly defined interaction type
> (donor vs. acceptor), secondary interactions (usually steric clashes) that
> destabilize the water interaction, or simply an unfavorable environment due
> to the local electronic structure. Observations from visual inspection can
> be used to troubleshoot the input settings or exclude particular target
> data from the optimization´.
>
> Maybe Orca supersedes this ffTK excerpt above towards the .inp Charge
> adjustments, I do not know ,any insight would be appreciated, (I had
> similarly posted this inquiry within the Orca Forum without a response
> as-of-yet), thanks:)
>
> Joel [image: 🚀]
>
>
> https://urldefense.com/v3/__https://www.dropbox.com/scl/fo/h8md4e915mce6pif2qmup/ABGJBwN77MO97GAJuigSCdU?rlkey=e9gv6lm59x87g1pjtckl06mpd&st=epnerg60&dl=0__;!!DZ3fjg!-ry1Z8TAK-Td2hSIJLX-AxbH6ViFIMbFF1TYXgA9KIX4P70NjmAFJ4QfaGgJVrkwIzgRu2VRo_H7xqoexs9GgcB0ZA$
> <https://urldefense.com/v3/__https://www.dropbox.com/scl/fo/h8md4e915mce6pif2qmup/ABGJBwN77MO97GAJuigSCdU?rlkey=e9gv6lm59x87g1pjtckl06mpd&st=epnerg60&dl=0__;!!DZ3fjg!6biUWE2vUrMnSvzLXrluLMvyXG6CIB4e2nTvYBE-50LPjw4Lk8EanFS4zgaoIDExhWVZVLFr8svdM-fRnppuzi5Z5A$>
>