how to get Charge of new residue?

From: yxiong_at_mail.ccnu.edu.cn
Date: Fri Nov 28 2003 - 23:29:34 CST

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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