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

From: David A Case <>
Date: Sat, 14 Aug 2021 07:41:15 -0400

On Fri, Aug 13, 2021, Rana Rehan Khalid wrote:

>I have a nucleotide lets consider guanine and I want to cap the basepairing
>(G-C) atoms of guanine. And want to study the affect of other 2 atoms on
>the protein surface. How can I do this. I actually want, not to allow
>basepairing atoms to interact with surface residue.

You'll probably have to think more carefully about what you want to
accomplish. What (exactly) do you mean when you say that certain atoms
don't "interact" with other atoms or residues? Are you trying to eliminate
hydrogen bonds between the guanine and the protein? Or something else?


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Received on Sat Aug 14 2021 - 05:00:02 PDT
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