Re: [AMBER] Recurring problem: Ligand lose planarity

From: Jenny 148 <>
Date: Tue, 28 Apr 2020 00:21:53 +0530

It is a huge distortion. The minimisation and heating average structures
are fine. But the equilibration and production average struvtures are
distorted. Snapshots from various frames of the production also shows this.
The esp calculated gout file was converted to prepi and pdb using
On 27 Apr 2020 23:53, "David A Case" <> wrote:

> 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
> planar.
> Of course, if you have large deviations from planarity, then checking
> how you obtained your atom types is worthwhile.
> ....dac
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Received on Mon Apr 27 2020 - 12:00:03 PDT
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