AMBER Archive (2004)

Subject: Re: AMBER: BOND energy during minimisation

From: David A. Case (
Date: Tue Oct 19 2004 - 09:59:46 CDT

On Tue, Oct 19, 2004, cailliez wrote:
> When I am doing minimization under constraint with AMBER7, it appears
> that BOND energy is increasing dramatically, which I do not understand.
> I have this same behavior with all my systems, so I guess it is not due
> to it.

I'm assuming that all of the test cases pass, so that in fact, the behavior
you see probably _is_ something to do with how you are preparing your systems.
It does look like you have a very bad starting structure (high bond energy,
high vdW energy...) Also, getting -1 million kcal of electrostatic energy
looks wrong to me. You may want to do some intial (constrained) minimization
in vacuum (or GB) prior to solvating the system.

...good luck...dac

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