VMD-L Mailing List
From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Mon Nov 04 2024 - 09:16:41 CST
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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: 🚀]
- Next message: Rajahmundry Ganesh Kumar ch20d408: "Volume considered in calculation of g(r)"
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- Next in thread: Joel Subach: "Re: ffTK Water Int Tab .inp File dropping the Charge Value from -2 to 0 Inquiry?"
- Reply: Joel Subach: "Re: ffTK Water Int Tab .inp File dropping the Charge Value from -2 to 0 Inquiry?"
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