[AMBER] contacts with water

From: Chinthaka Ratnaweera <cnr88.msstate.edu>
Date: Thu, 1 Jan 2015 22:51:31 -0600


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

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Received on Thu Jan 01 2015 - 21:00:02 PST
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