Hello,
I'm trying to model co-assembly of two different molecules. My simulations are set up using 10 molecules of each type. I've noticed one of the molecules tends to appear more on the surface, and the other more in the core of an aggregate. I would like to analyze or map their contacts with each other to understand how the structure may be stabilized.
However, as far as I know, the best way to map contacts is using the native contacts command in cpptraj. The problem with this is the gnuplot file generated for a contact map between 20 molecules is very difficult to visualize and occasionally makes gnuplot crash. Is there a way to look at the most frequent contacts per molecule and average values for each molecule type? Or is there a way to plot only the top 20 or so contacts?
I've tried a simulation with only one molecule of each type, but the results are not very meaningful. Any feedback is appreciated!
Thank you,
Naxhije Berisha
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Received on Fri Oct 23 2020 - 11:00:01 PDT
