AMBER Archive (2009)

Subject: Re: [AMBER] High energy during minimization

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Sun May 03 2009 - 08:40:22 CDT

On Sun, May 03, 2009, aneesh cna wrote:
>
> I am using Amber 9.0 version. My system contains molecule having
> benzene ring as a part of it.My leap went through with some unusual warnings
> like '*1-4: angle 12388 12392 duplicates bond ('triangular' bond) or angle
> ('square' bond)'

Unless you actually have three-atom or four-atom rings in your structure, you
will need to figure out what is causing these messages. I think they give atom
numbers, so you probably find their location easily. (You can also load the
prmtop file into VMD, and it will show the bonds that are in the prmtop file.)

Without more information, I can't speculate on what might be causing the
warnings themselves.

...dac

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