Re: [AMBER] How to cap the residue/ nucleotide atoms

From: David A Case <>
Date: Sat, 28 Aug 2021 16:47:33 -0400

On Sat, Aug 28, 2021, Rana Rehan Khalid wrote:

>Yes you are right I actually want to eliminate hydrogen bond of some
>guanine atoms (not all) so that those atoms not interact with protein.
>Kindly guide how can I do this. Thanks

I've got no ideas right now. You might think about changing the charges on
some of the guanine atoms, so that there is no electrostatic attraction to
potential hydrogen bond partners. (This would affect all interactions, not
just potential partners on the protein, but also with water or other nucleic

Don't be afraid to experiment. But this is definitely not any kind of
standard modification, so you should expect a trial and error experience to
get things to do work they way you want.

Maybe someone on the list has a different idea here.


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Received on Sat Aug 28 2021 - 14:00:02 PDT
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