Re: [AMBER] Average structure vs Individual frames

From: David A Case <>
Date: Tue, 14 May 2019 09:09:05 -0400

On Tue, May 14, 2019, Yin, Guowei wrote:
>My protein contains GDP and Mg2+. After the simulation, I look up the
>individual frames and the average structure over the 50 ns. I found in
>the individual frames the Mg2+ stays close to the phosophates of GDP and
>leads to the artificial bonds recognized by the PyMol. But in the average
>structure, the distance looks fine and no artificial bonds by PyMol. I
>attached the screenshot below. This is something with the processing?

Get an average structure where there is lots of motion can lead to quite
strange results: the average structure might not mean much is waters or
ions are moving around.

The "artificial bonds" are likely visualization artifacts: the force
field doesn't have any bonds between Mg and GDP, but pymol might draw a
connection if the distance is close.

...hope this helps...dac

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Received on Tue May 14 2019 - 06:30:03 PDT
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