[AMBER] Electrostatic distance plot

From: Sruthi Sudhakar <sruthisudhakarraji.gmail.com>
Date: Wed, 23 Dec 2020 09:28:14 +0530

Dear all,
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.

Thank you.
Sruthi Sudhakar
AMBER mailing list
Received on Tue Dec 22 2020 - 20:00:02 PST
Custom Search