VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Sat Nov 09 2024 - 23:35:46 CST

Hello VMD Community,

After further analysis I believe the solution to the above thread is
fly-aways generated via steric hindrance of the ligand charge depending on
whether the water molecule is a donor or acceptor, accordingly I believe
the charge in this instance can be modulated. Feel free to inquire
further for a more detailed explanation if in need, thanks:), Joel[image:
🚀]

On Fri, Nov 8, 2024 at 10:52 AM Joel Subach <mjsubach_at_alumni.ncsu.edu>
wrote:

> ...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!9FdPnuVDvyzFlnW1lHRfJjyWA6jhow8i4vGhHtL9vZef0Z2jPqQTfrKmlA0JYMmVHCwBtIp9cRx71cl3zl9TLtF8GA$
>
> 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!9FdPnuVDvyzFlnW1lHRfJjyWA6jhow8i4vGhHtL9vZef0Z2jPqQTfrKmlA0JYMmVHCwBtIp9cRx71cl3zl-9rVnRFQ$
>>>> <https://urldefense.com/v3/__https://www.dropbox.com/scl/fo/h8md4e915mce6pif2qmup/ABGJBwN77MO97GAJuigSCdU?rlkey=e9gv6lm59x87g1pjtckl06mpd&st=epnerg60&dl=0__;!!DZ3fjg!6biUWE2vUrMnSvzLXrluLMvyXG6CIB4e2nTvYBE-50LPjw4Lk8EanFS4zgaoIDExhWVZVLFr8svdM-fRnppuzi5Z5A$>
>>>>
>>>