Re: [AMBER] Warning regarding "triangular bond"

From: Bill Ross <>
Date: Wed, 16 Dec 2015 11:45:48 -0800

> 1-4: angle 2656 2657 duplicates bond ('triangular' bond)...

I should have added "[not water]" to that warning.


On 12/16/15 4:57 AM, David A Case wrote:
> 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.
> ...dac
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Received on Wed Dec 16 2015 - 12:00:03 PST
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