Hi Users,
I was reading through some mailing list archives whereby people have suggested using the "rms2d" tool of cpptraj to analyse the conformational space diversity before even going to clustering.
What I could not understand from the output of the rms2d tool i show to interpret it and which rms value can be used as a threshold to identify structurally similar structures versus different conformations.
I just ran it on 10 frames of my simulation and I get an output like this. I am using a GLUTAMATE "O" atom as it is in one of my main hotspot sites.
#Frame 1 2 3 4 5 6 7 8 9 10
1 0.000 0.062 0.102 0.118 0.104 0.099 0.063 0.081 0.066 0.067
2 0.062 0.000 0.124 0.097 0.086 0.062 0.057 0.061 0.080 0.033
3 0.102 0.124 0.000 0.182 0.124 0.145 0.085 0.129 0.079 0.108
4 0.118 0.097 0.182 0.000 0.100 0.061 0.124 0.077 0.115 0.105
5 0.104 0.086 0.124 0.100 0.000 0.069 0.090 0.048 0.070 0.075
6 0.099 0.062 0.145 0.061 0.069 0.000 0.078 0.055 0.085 0.058
7 0.063 0.057 0.085 0.124 0.090 0.078 0.000 0.077 0.056 0.034
8 0.081 0.061 0.129 0.077 0.048 0.055 0.077 0.000 0.061 0.056
9 0.066 0.080 0.079 0.115 0.070 0.085 0.056 0.061 0.000 0.065
10 0.067 0.033 0.108 0.105 0.075 0.058 0.034 0.056 0.065 0.000
~
~
Debarati
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Received on Tue Apr 02 2019 - 12:00:03 PDT
