AMBER Archive (2005)

Subject: AMBER: ibelly not working

From: Stern, Julie (jvstern_at_bnl.gov)
Date: Wed Apr 20 2005 - 14:40:28 CDT

Hello,
   My pinned atoms using ibelly (which I know designates what should
move rather than what stays frozen) don't appear pinned at all. Below
are the coordinates for 2.5 ps and for 150 ps and there are discrepencies
in as high as the 1st decimal place. Is something wrong with the
ibelly pinning procedure? I thought when an atom is frozen it would have
the exact same coordinates out to however many decimals there are.

Any advice?

Thanks.

--Julie

2.5 ps:
ATOM 17 A17 TSS X 0 3.622 3.549 3.549 1.00 0.00
ATOM 36 A36 TSS X 0 3.621 3.550 24.119 1.00 0.00
ATOM 53 A17 TSS X 1 8.590 3.550 3.551 1.00 0.00
ATOM 72 A36 TSS X 1 8.590 3.550 24.120 1.00 0.00
ATOM 89 A17 TSS X 2 13.560 3.549 3.550 1.00 0.00
ATOM 108 A36 TSS X 2 13.560 3.550 24.118 1.00 0.00
ATOM 125 A17 TSS X 3 18.532 3.551 3.551 1.00 0.00
ATOM 144 A36 TSS X 3 18.530 3.551 24.119 1.00 0.00
ATOM 161 A17 TSS X 4 23.500 3.550 3.549 1.00 0.00
ATOM 180 A36 TSS X 4 23.499 3.552 24.120 1.00 0.00
ATOM 197 A17 TSS X 5 28.470 3.550 3.552 1.00 0.00
ATOM 216 A36 TSS X 5 28.471 3.551 24.118 1.00 0.00

150 ps:
ATOM 17 A17 TSS X 0 3.667 3.605 3.596 1.00 0.00
ATOM 36 A36 TSS X 0 3.576 3.596 24.103 1.00 0.00
ATOM 53 A17 TSS X 1 8.592 3.670 3.526 1.00 0.00
ATOM 72 A36 TSS X 1 8.572 3.579 24.187 1.00 0.00
ATOM 89 A17 TSS X 2 13.488 3.559 3.538 1.00 0.00
ATOM 108 A36 TSS X 2 13.535 3.501 24.117 1.00 0.00
ATOM 125 A17 TSS X 3 18.436 3.492 3.585 1.00 0.00
ATOM 144 A36 TSS X 3 18.514 3.560 24.200 1.00 0.00
ATOM 161 A17 TSS X 4 23.567 3.467 3.501 1.00 0.00
ATOM 180 A36 TSS X 4 23.593 3.451 24.121 1.00 0.00
ATOM 197 A17 TSS X 5 28.514 3.544 3.490 1.00 0.00
ATOM 216 A36 TSS X 5 28.378 3.607 24.039 1.00 0.00

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