Re: how to get Charge of new residue?

From: yxiong_at_mail.ccnu.edu.cn
Date: Sun Nov 30 2003 - 03:51:26 CST

Thank many people's answer on charge and HIS forms!

However, I know the protein residues in the topology file are not free amino
acids, but the corresponding section in a polypeptide. I just don't know which
molecule(A or B) I should use for my new residue (carbamylated Lys-169) to
calculate the charge?:
        COOH
> > |
> > H2N-C-H
> > |
> > (CH2)4NHCO2
> > (A)
> > as
> > CO
> > |
> > HN-C-H
> > |
> > (CH2)4NHCO2 (B)

 If I use B because it is the corresponding section, CO will go far away from this
molecule.
  That is to say, when deciding the charge of residue of protein, which molecule
will be used to calculate, free amino acid or section?
  Thanks a lot!

>From: Fangqiang Zhu <fzhu_at_ks.uiuc.edu>
>Reply-To:
>To: yxiong_at_mail.ccnu.edu.cn
>Subject: Re: namd-l: how to get Charge of new residue?
>
>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 dont 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-169s charge, from (A) or
(B)?
> >
> > Thank you for your help!
>
>

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