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

From: Rana Rehan Khalid <>
Date: Sat, 28 Aug 2021 15:28:42 -0400

Dear Sir

I am actually waiting for your response, due to some reason email goes to
junk mail,
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
Kind Regards

On Sat, 14 Aug 2021, 7:41 am David A Case, <> wrote:

> 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?
> ....dac
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Received on Sat Aug 28 2021 - 12:30:03 PDT
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