Re: Acetyl group patch for lysine residue

From: ehenriques_at_qui.uc.pt
Date: Mon May 17 2010 - 03:56:01 CDT

Quoting Prija Ponnan <prija.ponnan_at_gmail.com>:

> Hello
>
> I want to study the effect of post-translational modification of by way of
> acetylation of epsilon-lysine residues by simulation using NAMD.For this
> purpose, I want to use acetyl group patch (ACE patch) to lysine residues of
> protein in the .psf file.
> Please guide me.
>
> --
> Prija Ponnan
>

Hi,

If I understand you correctly, you want to create
N(epsilon)-Acetyl-L-lysine residues, right? If that is the case, then
the ACE patch is not readily applicable as it is: you can build your
own patch using ACE as a template, but you need to modify it in order
to delete two of the hydrogens atoms of the -NH3+ group of lysine and
then make a bond between the NZ atom and the acetyl group.

E.

-- 
Elsa S. Henriques                     e-mail: ehenriques_at_qui.uc.pt
Investigadora Auxiliar
Biologia Estrutural e Computacional (@CNC)
e Grupo de Química Estrutural (@CCC)
Cv15 - RMB Lab
Departamento de Química - Universidade de Coimbra
3004-535 COIMBRA                         Portugal
Tel.: +351 23 9852080 - ext.417
Fax : +351 23 9827703

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