AMBER Archive (2005)

Subject: AMBER: Amber parameters for ADP

From: zgleo (zgleo_at_tom.com)
Date: Sat Jul 30 2005 - 00:22:19 CDT

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_at_gmail.com
___________________________________________

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