Dear amber-users，
Has anybody used the ADP parameters of Carlson (
http://pharmacy.man.ac..uk/amber/)? I found that the topology of the molecule is not correct while viewing in xLeap. I don't know if this is relevant for the use of the parameter. Can anyone give some idea?
Here is the prep file.
====================================================================================
0 0 2
R-ADENOSINE - with diphosphate linker
adp.db94
adp INT 1
CORRECT OMIT DU BEG
0.0
1 DUMM DU M 0 0 0 0.000 0.000 0.000 0.000
2 DUMM DU M 1 0 0 1.000 0.000 0.000 0.000
3 DUMM DU M 2 1 0 1.000 90.000 0.000 0.000
4 O1B O3 M 3 2 1 1.000 90.000 180.000 -0.9552
5 PB P M 4 3 2 1.434 90.000 180.000 1.3672
6 O2B O3 E 5 4 3 1.574 107.490 -79.441 -0.9552
7 O3B O3 E 5 4 3 1.518 118.007 165.990 -0.9552
8 O3A OS M 5 4 3 1.599 113.374 180.000 -0.6346
9 PA P M 6 5 4 1.646 130.619 36.624 1.4929
10 O1A O2 E 7 6 5 1.504 109.212 -90.234 -0.9474
11 O2A O2 E 7 6 5 1.526 108.570 40.323 -0.9474
12 O5* OS M 7 6 5 1.585 97.173 157.726 -0.6579
13 C5* CT M 8 7 6 1.445 122.292 -66.317 0.0558
14 H50 H1 E 9 8 7 1.059 109.484 27.531 0.0679
15 H51 H1 E 9 8 7 1.059 109.437 -92.456 0.0679
16 C4* CT M 9 8 7 1.477 113.286 147.538 0.1065
17 H40 H1 E 16 9 8 1.059 105.768 -179.178 0.1174
18 O4* OS S 16 13 9 1.482 106.235 -62.889 -0.3548
19 C1* CT B 18 16 13 1.391 107.688 128.804 0.0394
20 H10 H2 E 19 18 16 1.059 109.468 91.228 0.2007
21 N9 N* S 19 18 16 1.552 105.091 -143.300 -0.0251
22 C8 CK B 21 19 18 1.388 123.797 33.434 0.2006
23 H80 H5 E 22 21 19 1.078 131.047 -3.389 0.1553
24 N7 NB S 22 21 19 1.384 108.967 176.598 -0.6073
25 C5 CB S 24 22 21 1.395 103.021 0.702 0.0515
26 C6 CA B 25 24 22 1.412 128.288 178.252 0.7009
27 N6 N2 B 26 25 24 1.333 125.907 -3.791 -0.9019
28 H60 H E 27 26 25 1.010 120.010 2.829 0.4115
29 H61 H E 27 26 25 1.009 120.014 -177.167 0.4115
30 N1 NC S 26 25 24 1.343 113.319 178.851 -0.7615
31 C2 CQ B 30 26 25 1.340 123.433 -1.664 0.5875
32 H2 H5 E 31 30 26 1.077 120.022 -177.875 0.0473
33 N3 NC S 31 30 26 1.377 125.379 2.123 -0.6997
34 C4 CB E 33 31 30 1.300 108.242 -0.035 0.3053
35 C3* CT M 16 13 12 1.484 117.051 57.581 0.2022
36 H30 H1 E 35 16 13 1.059 117.939 24.820 0.0615
37 O3* OH S 35 16 13 1.407 108.509 149.908 -0.6541
38 H3* HO E 37 35 16 0.967 109.470 163.254 0.4376
39 C2* CT M 35 16 13 1.607 102.425 -96.715 0.0670
40 H20 H1 E 39 35 16 1.059 115.086 78.119 0.0972
41 O2* OH S 39 35 16 1.398 114.943 -153.294 -0.6139
42 H2* HO E 41 39 35 0.967 109.456 -41.679 0.4186
IMPROPER
C8 C4 N9 C1*
C6 H60 N6 H61
N7 N9 C8 H80
N1 N3 C2 H2
C5 N1 C6 N6
LOOP CLOSING EXPLICIT
C1* C2*
C4 C5
C4 N9
DONE
STOP
=====================================================================================
Best regard!
zgleo
2005-07-30
___________________________________________
Zhiguo Liu
Ph.D candidate
Drug Discovery and Design Center
Shanghai Institute of Materia Medica
Chinese Academy of Science
Shanghai, China
zhiguo.leo.gmail.com
___________________________________________
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Received on Sat Jul 30 2005 - 06:53:01 PDT
