Hi
I want to determine the interactions of a coordinated metal ion (Ca) in a
protein during a MD simulation. Through visualization of the trajectory I
noted that water molecules are also a part of the coordination sphere. I
tried to find the contacts with nativecontacts and contact commands in
cpptraj but it gives only the contacts with protein but not the water
molecules. (says nothing selected for ':WAT')
Is there a way I can find all the contacts including those with water?
Thank you
Chinthaka
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Received on Thu Jan 01 2015 - 21:00:02 PST
