Re: [AMBER] Planarity of bound versus unbound ligand

From: David Case <>
Date: Tue, 12 Feb 2019 01:57:39 +0000

On Mon, Feb 11, 2019, Tye Martin wrote:

>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?

Assuming I understand your question:

This sort of thing is done all the time: if there is not a bond-path
connecting the four atoms, then it is generally called a
"pseudo-dihedral", but cpptraj doesn't care.

[Of course, this doesn't mean that your particular choice of atoms will
give you the information you want--devil is in the details.]


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Received on Mon Feb 11 2019 - 18:00:01 PST
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