VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Mon Jul 08 2024 - 04:51:34 CDT

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