[AMBER] Planarity of bound versus unbound ligand

From: Tye Martin <tmarti16.unm.edu>
Date: Mon, 11 Feb 2019 20:36:42 +0000

I am simulating a system with an amyloid protein and a phenylene ethynylene oligomer. I would like to look at the planarization of the ring groups of the ligand over time but the dihedrals are separated by multiple atoms. Would it be valid to choose a dihedral that isn't four atoms in a row to determine the restriction of rotation when bound to the protein surface?

Thank you for your help.
Tye Martin

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Received on Mon Feb 11 2019 - 13:00:03 PST
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