Re: problem at maintaining geometry coordinate

From: Kwee Hong (joyssstan0202_at_gmail.com)
Date: Tue Aug 17 2010 - 23:43:25 CDT

Sorry, this is an incomplete post... The complete one would be sent out
later. So sorry...

On Wed, Aug 18, 2010 at 11:48 AM, Kwee Hong <joyssstan0202_at_gmail.com> wrote:

> 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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