From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Tue Aug 17 2010 - 22:48:35 CDT
Hi all,
I'm trying to simulate a metallothionein which is bound to 3 cadmium ion
with its 9 cysteines. Each cadmium is coordinated tetrahedrally by 4
cysteines. As cadmium is not found in the topology, I've added the relevant
info manually:
MASS 107 CAD 112.410000 CAD! cadmium ion
RESI CAD 2.00 ! Cadmium ion
GROUP
ATOM CAD CAD 2.00
PATCHING FIRST NONE LAST NONE
As the cysteines in the protein are deprotonated and bound to either one or
two cadmium, they have been defined in the topology, too by the name CYT
(terminal thiol) and CYB (bridging thiol):
RESI CYB -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 S1 -0.80 ! |
GROUP
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA SG CB N HN N CA
BOND C CA C +N CA HA CB HB1 CB HB2
DOUBLE O C
IMPR N -C CA HN C CA +N O
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982
IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202
IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498
IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306
IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548
IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584
IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837
IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359
IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134
IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124
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
BOND CB CA SG CB N HN N CA
BOND C CA C +N CA HA CB HB1 CB HB2
DOUBLE O C
IMPR N -C CA HN C CA +N O
DONOR HN N
ACCEPTOR O C
IC -C CA *N HN 1.3479 123.9300 180.0000 114.7700 0.9982
IC -C N CA C 1.3479 123.9300 180.0000 105.8900 1.5202
IC N CA C +N 1.4533 105.8900 180.0000 118.3000 1.3498
IC +N CA *C O 1.3498 118.3000 180.0000 120.5900 1.2306
IC CA C +N +CA 1.5202 118.3000 180.0000 124.5000 1.4548
IC N C *CA CB 1.4533 105.8900 121.7900 111.9800 1.5584
IC N C *CA HA 1.4533 105.8900 -116.3400 107.7100 1.0837
IC N CA CB SG 1.4533 111.5600 180.0000 113.8700 1.8359
IC SG CA *CB HB1 1.8359 113.8700 119.9100 107.2400 1.1134
IC SG CA *CB HB2 1.8359 113.8700 -125.3200 109.8200 1.1124
IC CA CB SG CAD 1.5380 112.5000 60.0000 95.9000 2.5600
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