charge calculation

From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Sat Aug 28 2010 - 09:09:12 CDT

Hi.

I have defined a new residue in the parameter file with following charges:

RESI CYT -1.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1
ATOM HA HB 0.09 ! | | -
GROUP ! HA-CA--CB--SG (thiolate)
ATOM CB CS -0.38 ! | |
ATOM HB1 HA 0.09 ! | HB2
ATOM HB2 HA 0.09 ! O=C
ATOM SG SS -0.80 ! |
GROUP
ATOM C C 0.51
ATOM O O -0.51

It's actually a deprotonated cysteines where the CB and SG have different
charges as compared to the RESI CYS.

4 CYT is then patched to 1 cadmium ion:

PRES TETR -1.60
GROUP
ATOM 1CAD CAD 1.20
GROUP
ATOM 2SG SS -0.60
GROUP
ATOM 3SG SS -0.60
GROUP
ATOM 4SG S1 -0.60
GROUP
ATOM 5SG S1 -0.60

Now I would like to know is the charge at each RESI CYT equal to -0.8 and
the charge of each metal-thiolate center is equal to -2?

Thanks.

Regards,
Joyce

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