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
