I think it was confusing that you said it was an "electrostatic distance
plot" but really this is just a distance plot. If you are looking to
analyze hydrogen bonds, cpptraj has that ability and can provide much more
detailed information that seen in your distance plot. The cpptraj manual
has details, and there are tutorials available.
On Wed, Dec 23, 2020 at 9:19 AM Sruthi Sudhakar <
sruthisudhakarraji.gmail.com> wrote:
> Dear prof. Case,
> The cut off merely means that in the plot if the distance of 3.5 angstroms
> or less is maintained, it was considered to be a good electrostatic
> interaction in the system throughout the simulation. This notion was
> considered referring some previous publications. Hope the attachment is now
> visible to you.
>
>
> On Wed, 23 Dec 2020 at 7:38 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
> > On Wed, Dec 23, 2020, Sruthi Sudhakar wrote:
> >
> > >I have been calculating the electrostatic distance plot between the
> > >protonated nitrogen atom of my ligand and the negatively charged
> backbone
> > >of DNA in a DNA-ligand complex. The distance was calculated using the
> > >distance option in cpptraj. The protonated nitrogen belongs to the
> > >pyrrodiline ring at the end of a propyl chain. The plot between the N+
> and
> > >OP is attached here. If the cut off of 3.5 angstroms is considered are
> > the
> > >high fluctuations (10-20 angstroms) seen in the plot possible or is it
> > some
> > >discrepancy? Kindly advise on the above.
> >
> > Nothing was attached...you might also be more specific about what you
> > mean a "cut off of 3.5 angstroms"....
> >
> > ....dac
> >
> >
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Received on Wed Dec 23 2020 - 07:30:02 PST
