Re: [AMBER] Electrostatic distance plot

From: David A Case <>
Date: Wed, 23 Dec 2020 09:07:26 -0500

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 might also be more specific about what you
mean a "cut off of 3.5 angstroms"....


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Received on Wed Dec 23 2020 - 06:30:03 PST
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