Thank you, Daniel
Núbia
________________________________
De: Daniel Roe <daniel.r.roe.gmail.com>
Enviado: terça-feira, 20 de fevereiro de 2018 14:18
Para: AMBER Mailing List
Assunto: Re: [AMBER] "Issue" with hbond
Hi,
On Fri, Feb 16, 2018 at 4:57 PM, Núbia Prates <nnubiaits.hotmail.com> wrote:
> As result, I was expecting a total of 11 hydrogen bonds, but analyzing the backbone.lifetime.xvg file I got extra interactions, for instance for the residues GLU142 and LYS264 (I was expecting 2 hbond):
>
> GLU_142.OE1-LYS_264.NZ-HZ1
> GLU_142.OE2-LYS_264.NZ-HZ1
> GLU_142.OE1-LYS_264.NZ-HZ2
> GLU_142.OE2-LYS_264.NZ-HZ2
> GLU_142.OE1-LYS_264.NZ-HZ3
> GLU_142.OE2-LYS_264.NZ-HZ3
Why were you only expecting 2 hydrogen bonds here? Glu has 2 potential
hydrogen bond acceptors (OE1 and OE2) and Lys has 3 potential
hydrogens to donate (HZ1-3), so there are 6 potential hydrogen bonds
(and indeed that is what you see). The only reason you would get fewer
hydrogen bonds is if one or both amino acids were constrained somehow
(by e.g. steric clashes).
-Dan
>
> I can't understand this result. Can anyone help me with that?
> Regards
> Nubia
>
>
>
>
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Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
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Received on Tue Feb 20 2018 - 10:30:03 PST
