Sir,
Sorry for the confusion. It is a distance plot between the N+ atom and
phosphate of the backbone. These are expected to show electrostatic
interactions since the backbone is negative. The script we have used for
this calculation is
parm comsol.prmtop
trajin prod.nc
rms first :1-23
distance :14.OP2 :1.N4 out distance4_14_OP2.dat
And I got the plot attached. But the value ranges in between 2-20
angstroms. Is it likely to have such values ?
Regards,
Sruthi Sudhakar
On Wed, Dec 23, 2020 at 8:34 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
> > >
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 23 2020 - 08:00:02 PST
