[AMBER] Hydrophobic interaction VS time in protein interfaces

From: Jag Silwal <jagsilwal.gmail.com>
Date: Tue, 9 Jan 2018 11:45:38 -0500

Dear all,

I just finished a long simulation of a protein-protein complex and I would
like to plot a 'number of hydrophobic interactions Vs Time'. How do I
calculate hydrophobic interactions? I don't see a separate section for this
in manual and I suppose it is incorporated in PB/GBSA calculation but I am
not quite clear on how to go about this.

And also, to get a plot for 'number of hydrogen bonds VS time' do I just do
the lifetime analysis as mentioned in the tutorial?

The type of plot I am trying to get is similar to the one mentioned in this

article (Figure 3 and 4) :

Thank you for your help.

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Received on Tue Jan 09 2018 - 09:00:02 PST
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