Re: [AMBER] Recurring problem: Ligand lose planarity

From: David A Case <>
Date: Mon, 27 Apr 2020 14:23:18 -0400

On Sun, Apr 26, 2020, Sruthi Sudhakar wrote:

>my aromatic ligand also shows planarity distortion.

Is this a big distortion from planarity or just a small one? Is it in a
snapshot for MD or in a fully-minimized structure?

This is just a guess, but many people are so used to seeing models with
perfectly planar aromatic groups, that even small deviations are a
course of concern. It is only the average structure that should be

Of course, if you have large deviations from planarity, then checking
how you obtained your atom types is worthwhile.


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Received on Mon Apr 27 2020 - 11:30:02 PDT
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