[AMBER] Normal Mode Analysis - output from nmode?

From: Robert DeLisle <rkdelisle.gmail.com>
Date: Sat, 24 Mar 2018 11:42:51 -0600

I'm attempting to perform Normal Mode Analysis using nmode as described in
chapter 39.4 of the Amber manual. I have successfully run the scrip shown
at the end of chapter 39.4 using my own protein, but there I'm not sure how
to interpret the final output.

The conjgrad and newton steps are obvious, but for the final nmode call, I
see the following output:

     1 -24.811
     2 -11.550
     3 -8.155
     4 -6.698
     5 -5.157
     6 -4.132
     7 -3.205
     8 -2.037
     9 -1.273
    10 -0.547
    11 -0.000
    12 0.000
    13 0.000
    14 1.038
    15 2.073
    16 5.582
    17 6.925 0.592 1.986 8.734
    18 7.556 0.592 1.986 8.561
    19 7.689 0.592 1.986 8.526
    20 8.634 0.592 1.986 8.296
    21 8.941 0.592 1.986 8.227
    22 9.289 0.592 1.986 8.151
    23 9.602 0.592 1.986 8.085
    24 9.759 0.592 1.986 8.053
    25 10.079 0.592 1.985 7.989
    26 10.844 0.592 1.985 7.843
    27 11.305 0.592 1.985 7.761
    28 11.923 0.592 1.985 7.655
...

with a total of 2490 lines. I assume that each line represents each atom
in my protein, but I have not been able to find an interpretation of the
columns.

Ultimately, I would like to take the results from the normal mode analysis
and write out an Amber trajectory file that could be used in PCAsuite (
http://mmb.pcb.ub.es/software/pcasuite/pcasuite.html) for further analysis.

Any assistance in appreciated.

-Robert Kirk DeLisle
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Received on Sat Mar 24 2018 - 11:00:02 PDT
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