Dear amber users,
The question I want to ask is not directly about amber. But I think there
should be somebody here who is familar with Curves.
I use curves to analyze average DNA duplex (with drug bound with
bonding ) produced by MD simulation by sander.
First question is about groove parameter. I don't understand the 'n' value
in the 'Levels' colum. If I want to get groove width or depth value for
each basepairs, can I just get the average value with same 'i' value ?
-----------------------
|K| Groove parameters |
-----------------------
Atom defining backbone: P 12 levels, 3 sub-levels
Levels Minor groove Major groove
i n Width Depth Angle Width Depth Angle Diam
C 1 0 -- -- -- C -- -- -- --
1 1 -- -- -- -- -- -- --
1 2 -- -- -- -- -- -- --
1 3 -- -- -- -- -- -- --
C 2 0 -- -- -- C -- -- -- 20.23
2 1 -- -- -- -- -- -- 20.14
2 2 -- -- -- -- -- -- 19.87
2 3 6.36 4.32 38 -- -- -- 20.10
T 3 0 6.87 4.20 34 T -- -- -- 20.60
3 1 7.30 4.29 34 -- -- -- 20.36
3 2 7.65 4.71 32 -- -- -- 20.24
3 3 7.94 5.01 32 15.51 2.90 67 20.24
C 4 0 8.28 4.61 36 C 13.92* 8.55 37 20.22
4 1 8.64 4.12 34 14.57 9.33 32 20.19
4 2 8.96 3.52 37 15.53 9.47 31 20.06
4 3 9.13 3.07 38 16.13 10.23 19 19.90
Second question is about 'over axis bending'. What does the "PP" & 'UU'
value stand for ? I should take which one as overall axis bending angle
value? And how do curves calculate the value?
Overall axis bend ... UU= 6.53 PP= 22.41
Third, I just remove the drug molecule bond to DNA for analysis, am I doing
rightly?
I would appreciate your kind reply. The question really bother me . Thank
you!
Best Wishes,
jane
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Received on Sun Jan 21 2007 - 06:07:54 PST
