VMD-L Mailing List

From: Joel Subach (mjsubach_at_alumni.ncsu.edu)
Date: Mon Jul 08 2024 - 12:04:35 CDT

Hello Pawel thank you so much for your kind informative update:).

Best,
Joel 🚀

On Mon, Jul 8, 2024 at 11:51 AM Paweł Kędzierski <
pawel.kedzierski_at_pwr.edu.pl> wrote:

> Dear Joel,
>
> Between 3 and 4 A sounds OK if you consider that the LJ radius of an
> aromatic carbon is about 2A and add 1.4 radius of water to that.
> However looking at your molecule I guess you may have some waters which
> are posed in such places that other groups are at similar distance or even
> closer than the interaction site. You should make sure that this not the
> case, for example by repositioning the water by modification of the
> internal coordinates in the gaussian (or orca) input file. Or if this is
> impossible, then consider parametrizing smaller fragments of your molecule.
> HTH,
> Pawel
>
> W dniu 8.07.2024 o 10:47, Joel Subach pisze:
>
> * 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
>>>
>>>
>
> --
> 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
>
>