AMBER Archive (2003)

Subject: Re: AMBER: frequency analysis

From: Piotr Cieplak (pcieplak_at_accelrys.com)
Date: Wed Jul 30 2003 - 16:49:08 CDT

My feeling is that you don't minimize your structure well enough
Piotr

Lishan Yao <yaolisha_at_pilot.msu.edu>
Sent by: owner-amber_at_scripps.edu
07/30/2003 02:43 PM
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Subject
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_at_pilot.msu.edu>
MSU

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