Hi,
One potential issue with the cpptraj input you posted is you have an
'rms' command before your 'distance' command. If your system has
periodic boundary conditions, cpptraj prints out a warning that
imaging is not possible after rotating the system. If you're
calculating an imaged distance, it will probably be warped by the
'rms'. Try putting the 'distance' command before 'rms' and see if that
helps things.
-Dan
On Wed, Dec 23, 2020 at 10:44 AM Sruthi Sudhakar
<sruthisudhakarraji.gmail.com> wrote:
>
> 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
> > > >
> > > >
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Received on Wed Dec 30 2020 - 07:00:03 PST
