Re: [AMBER] planarity issue during md

From: David A Case <>
Date: Mon, 15 Jun 2020 08:12:12 -0400

On Mon, Jun 15, 2020, Sofia Vasilakaki wrote:
>I simulated a small molecule which contains a similar to thymine ring,
>substituted by one C=O group. I generated partial charges in Gaussian.
>During simulation the amide N and some of the carbon atoms of the ring are
>not planar.

How far out of planarity are they? How did you assign atom types and
force field parameters?

One expects some deviations from base planarity during an MD simulation.
It's probably worth checking a minimization (of just the small molecule
itself) in order to see what the lowest-energy conformation looks like.


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Received on Mon Jun 15 2020 - 05:30:04 PDT
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