Hi, all,
Did any one notice that tree structure of TRP
amino acid in amber8?
In $AMBERHOME/dat/leap/prep/all_amino02.in, it
looks like:
.........
TRYPTOPHAN
TRP INT 1
CORR OMIT DU BEG
0.00000
1 DUMM DU M 0 -1 -2 0.000 0.000
0.000
2 DUMM DU M 1 0 -1 1.449 0.000
0.000
3 DUMM DU M 2 1 0 1.522 111.100
0.000
4 N N M 3 2 1 1.335 116.600
180.000
5 H H E 4 3 2 1.010 119.800
0.000
6 CA CT M 4 3 2 1.449 121.900
180.000
7 HA H1 E 6 4 3 1.090 109.500
300.000
8 CB CT 3 6 4 3 1.525 111.100
60.000
9 HB2 HC E 8 6 4 1.090 109.500
300.000
10 HB3 HC E 8 6 4 1.090 109.500
60.000
11 CG C* S 8 6 4 1.510 115.000
180.000
12 CD1 CW B 11 8 6 1.340 127.000
180.000
13 HD1 H4 E 12 11 8 1.090 120.000
0.000
14 NE1 NA B 12 11 8 1.430 107.000
180.000
15 HE1 H E 14 12 11 1.010 125.500
180.000
16 CE2 CN S 14 12 11 1.310 109.000
0.000
17 CZ2 CA B 16 14 12 1.400 128.000
180.000
18 HZ2 HA E 17 16 14 1.090 120.000
0.000
19 CH2 CA B 17 16 14 1.390 116.000
180.000
20 HH2 HA E 19 17 16 1.090 120.000
180.000
21 CZ3 CA B 19 17 16 1.350 121.000
0.000
22 HZ3 HA E 21 19 17 1.090 120.000
180.000
23 CE3 CA B 21 19 17 1.410 122.000
0.000
24 HE3 HA E 23 21 19 1.090 120.000
180.000
25 CD2 CB E 23 21 19 1.400 117.000
0.000
26 C C M 6 4 3 1.522 111.100
180.000
27 O O E 26 6 4 1.229 120.500
0.000
................
The tree label of atom CE2 is "S", and CD2 is
"E". That means there is no bond between CE2 and CD2,
Also no bond between CD2 and CG. But obviously, it's
not correct. I'm totally confused.
Thanks,
Yuhui
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Received on Thu Sep 02 2004 - 01:15:11 PDT
