AMBER Archive (2003)

Subject: RE: AMBER: frequency analysis

From: Yong Duan (yduan_at_udel.edu)
Date: Wed Jul 30 2003 - 18:04:00 CDT

 
My wild guess,
 
translation and rotation (6 degrees of freedom).
 
yong

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Piotr Cieplak
Sent: Wednesday, July 30, 2003 5:49 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: frequency analysis

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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