Re: AMBER: perturbed atoms are not bonded on using TIP5P wate

From: David A. Case <>
Date: Thu, 18 Jan 2007 09:40:37 -0800

On Wed, Jan 17, 2007, sugino tatsuro wrote:
> Still by using AMBER8, I compared two types of files, each of which is in
> the presence or absence of perturbation. As a result, in the file including
> perturbation the bond information was lost.

I'm wondering *exactly* what bond information is lost. I haven't been able
to reproduce your problem here. Note that it will appear that there are no
"perturbed" bonds if you are just doing something like changing the charges
on some atoms, but the regular bonds are still there, and should be applied
to both end points.

Does this problem exist if you just take a single TP5 water, perturb its
charges, and try to run it? We need to find the smallest test case, so that
you can post the prmtop file to really see what is going on, and so that
someone else can reproduce the problem.

In reality, I don't think people would be that surprised if there is some bug
in Amber 8 that keeps one from doing thermodynamic integration on systems with
extra points. If so, tracking that down is probably going to be a low
priority, given that the whole concept of perturbed prmtop files has been
removed from the current version.


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Received on Sun Jan 21 2007 - 06:07:24 PST
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