My feeling is that you don't minimize your structure well enough
Piotr
Lishan Yao <yaolisha.pilot.msu.edu>
Sent by: owner-amber.scripps.edu
07/30/2003 02:43 PM
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AMBER: frequency analysis
Hi there:
Last time, I posted an email about low frequencies I got from quasih
analysis for my ligand (6-hydroxymethyl-7,8-dihydropterin) in water. I
found one NH2 group and one CH2OH group spin. This may be the reason of
the low frequencies. But then I do the same analysis for ligand in
protein. I get similiar result. And there is not spin for both NH2 and
CH2OH. Can anyone explain why I have low frequencies here? And when I
look at the frequencies, I also see a big gap between 3cm-1 and 27cm-1.
I showed the result to my collegues, we could not get any idea about why
it is. So I show my result here. Any clue?
The rmsd compared to average structure is around 0.3A, so I assume I did
the right thing for the trajectory overlay.
freq. E Cv S
cm**-1 kcal/mol cal/mol-kelvin cal/mol-kelvin
--------------------------------------------------------------------------------
Total 22.400 72.307 276.379
translational 0.894 2.979 41.713
rotational 0.894 2.979 39.414
vibrational 20.612 66.349 195.252
1 0.479 0.596 1.986 14.052
2 0.493 0.596 1.986 13.994
3 0.508 0.596 1.986 13.936
4 0.552 0.596 1.986 13.769
5 0.763 0.596 1.986 13.126
6 1.224 0.596 1.986 12.187
7 2.041 0.596 1.986 11.172
8 27.459 0.597 1.983 6.012
9 28.848 0.597 1.983 5.914
10 33.317 0.597 1.982 5.628
11 37.904 0.597 1.980 5.373
12 41.472 0.598 1.979 5.195
13 44.296 0.598 1.978 5.064
14 55.002 0.599 1.974 4.637
15 58.316 0.600 1.973 4.521
16 66.424 0.601 1.969 4.265
17 74.655 0.602 1.965 4.035
18 76.084 0.602 1.964 3.997
19 79.477 0.603 1.962 3.912
20 89.330 0.605 1.956 3.683
21 95.590 0.606 1.951 3.551
22 102.191 0.608 1.947 3.420
23 104.781 0.608 1.945 3.372
24 115.190 0.611 1.936 3.188
25 118.082 0.612 1.934 3.140
26 124.367 0.613 1.928 3.040
27 128.689 0.615 1.924 2.974
28 131.274 0.615 1.921 2.936
29 136.559 0.617 1.916 2.860
30 149.612 0.621 1.903 2.686
31 161.300 0.625 1.890 2.543
32 166.444 0.627 1.884 2.484
33 178.094 0.632 1.869 2.357
34 190.596 0.637 1.853 2.231
--
Lishan Yao <yaolisha.pilot.msu.edu>
MSU
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Received on Wed Jul 30 2003 - 22:53:01 PDT
