Re: how to get Charge of new residue?

From: Fangqiang Zhu (fzhu_at_ks.uiuc.edu)
Date: Sat Nov 29 2003 - 01:03:31 CST

Hi,

The protein residues in the topology file are not free amino acids, but the
corresponding section in a polypeptide.

Zhu, Fangqiang

yxiong_at_mail.ccnu.edu.cn wrote:

> Dear sir,
> Because I must get the charge of carbamylated Lys-169 in my enzyme, so I must
> first optimize its configuration then get the charge.
>
> COOH
> |
> H2N-C-H
> |
> (CH2)4NHCO2
> However I find every amino acid residue in the topology is displayed as following
> and the according charges are given: ( I can understand this because every residue
> will connect with others.) I don't know which configuration these charges are
> generated in the topology file from, free amino acid or other form.
> CO
> |
> HN-C-H
> |
> R
>
> I just don¡¯t know whether I need display carbamylated Lys-169
> COOH
> |
> H2N-C-H
> |
> (CH2)4NHCO2
> (A)
> as
> CO
> |
> HN-C-H
> |
> (CH2)4NHCO2 (B)
> If yes, how should I calculate carbamylated Lys-169¡¯s charge, from (A) or (B)?
>
> Thank you for your help!

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