Re: [AMBER] Protein-nucleic acid interactions

From: Bill Ross <>
Date: Mon, 2 Nov 2020 22:23:00 -0800

There was an option to print the mden energies in a more-tabular form,
but my guess is you'd want e.g. group-group energetic terms, which might
be covered in MM-PBSA:


On 11/2/20 9:20 PM, Athena N wrote:
> Dear all,
> I am doing a series of protein nucleic acid system simulations and we are
> interested to learn more about the local non covalent interactions between
> the amino acids and the nucleic acid bases. I would like to know if there
> is some site from which we could get some input scripts to get the various
> non covalent interactions from the trajectory in AMBER. Are any scripts of
> that sort available in github? Please let me know. I am still learning to
> make amber inputs and mainly use the tutorials for that purpose. So if any
> such inputs are available, it would be of great help.
> Thanking you in advance.
> Athena
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Received on Mon Nov 02 2020 - 22:30:02 PST
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