From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Fri Nov 08 2024 - 03:52:27 CST

..and below is a shorter URL, maybe this will allow opening of the images:

https://urldefense.com/v3/__https://www.dropbox.com/scl/fo/h8md4e915mce6pif2qmup/ABGJBwN77MO97GAJuigSCdU?rlkey=e9gv6lm59x87g1pjtckl06mpd&st=m0mcdp5x&dl=0__;!!DZ3fjg!_d6OLBVHWTcVcy1DcyUIGqylwXjBC-HIWj02qcELOWAHS_RTPMZQAHCDnfVTb-rXiGOP04swt6aJgFKq4j_hY0EPUA$

On Wed, Nov 6, 2024 at 10:48 AM Joel Subach <mjsubach_at_alumni.ncsu.edu>
wrote:

> ...and I believe that the URL link is too long, precluding opening,
> accordingly attached are the three screenshots labeled, hopefully they
> appear, thanks:)
>
> On Tue, Nov 5, 2024 at 10:28 AM Joel Subach <mjsubach_at_alumni.ncsu.edu>
> wrote:
>
>> * 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!_d6OLBVHWTcVcy1DcyUIGqylwXjBC-HIWj02qcELOWAHS_RTPMZQAHCDnfVTb-rXiGOP04swt6aJgFKq4j_K7uxy7g$
>>> <https://urldefense.com/v3/__https://www.dropbox.com/scl/fo/h8md4e915mce6pif2qmup/ABGJBwN77MO97GAJuigSCdU?rlkey=e9gv6lm59x87g1pjtckl06mpd&st=epnerg60&dl=0__;!!DZ3fjg!6biUWE2vUrMnSvzLXrluLMvyXG6CIB4e2nTvYBE-50LPjw4Lk8EanFS4zgaoIDExhWVZVLFr8svdM-fRnppuzi5Z5A$>
>>>
>>