VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Mon Jul 08 2024 - 03:47:52 CDT

* from the INTERACTION site

On Mon, Jul 8, 2024 at 10:47 AM Joel Subach <mjsubach_at_alumni.ncsu.edu>
wrote:

> Hi Pawel thank you for your kind update:)
>
> Only a few of my results flew away completely i.e. many angstroms away,
> whereas I am seeming to have many interactions less than 4
> angstroms but more than 3 angstroms away from the insertion site although
> seeming to be placed correctly with the trajectory file.
> Accordingly would you recommend using the later still or discarding them
> as the former many angstroms away? (A screenshot of
> my molecule via Pymol is attached along with a text file.)
>
> Thanks if you know:),
> Joel 🚀
>
> On Mon, Jul 8, 2024 at 8:38 AM Paweł Kędzierski <
> pawel.kedzierski_at_pwr.edu.pl> wrote:
>
>> Dear Joel,
>> W dniu 7.07.2024 o 12:35, Joel Subach pisze:
>> > Hello VMD Community:),
>> >
>> > towards the above-topic, should I discard any of my QM optimized water
>> > interaction positions that settle into an area greater than a few
>> > angstroms from the interaction site?
>> If the water is repelled, then there is no interaction energy minimum at
>> the interaction site. Often, the interaction site was incorrectly
>> classified in FFTK as a donor while it should be an acceptor, or vice
>> versa. An example when this happens is with the nitro group, because
>> FFTK always considers nitrogen an acceptor and in -NO2 it is actually
>> positively charged.
>>
>> Otherwise, if the water is several angstroms away, the interaction
>> energy would be very small and inclusion of such result in the charge
>> optimization would just drive the respective partial charge close to
>> zero. In my opinion, it may only be useful when the interaction site is
>> indeed nonpolar and you need enough water interactions to prevent the
>> charge fitting to be under determined. An example when this is the case
>> is when the interaction site is a nonpolar hydrogen.
>> Cheers,
>> Pawel
>>
>> >
>> > Thanks if you know:),
>> > Joel 🚀
>>
>>
>> --
>> Room 3.03 A-3, tel. +48 71 320 3200
>> email: Pawel.Kedzierski_at_pwr.edu.pl
>> Institute of Advanced Materials I01W03D10
>> Faculty of Chemistry
>> Wrocław University of Science and Technology
>> Wrocław, Poland
>>
>>