Re: [AMBER] Warning regarding "triangular bond"

From: David A Case <>
Date: Wed, 16 Dec 2015 07:57:44 -0500

On Wed, Dec 16, 2015, Xiong Jiawei wrote:
> 1-4: angle 2656 2657 duplicates bond ('triangular' bond) or angle
> ('square' bond)
> I checked the prmtop file and found that the water molecules I added all
> looked like triangles. (meaning the two Hs also bonded to each other)

I think these two statements are (probably) not related to each other. You
should check what atoms are being referred to in the information messages you
are seing.

> Then I tried to follow the Amber Tutorial on using antechamber to do
> a trial to see where I went wrong. Surprisingly, I realized that this
> error is also shown on the tutorial web-page!

This is not a error, just an information message. Note that sustiva has a
cyclopropane group, and hence a "triangle" of bonds. The message is simply
saying that the angle terms are not needed, and is there since this is an
unusual situation, and might be indicative of an error in the connectivity.


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Received on Wed Dec 16 2015 - 05:00:03 PST
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