AMBER Archive (2006)

Subject: Re: AMBER: How did the coordinates change in xleap?

From: David A. Case (
Date: Tue Oct 17 2006 - 10:28:52 CDT

On Tue, Oct 17, 2006, Zhihong Yu wrote:
> In which step did the transformation of coordinates take place? loadpdb,
> solvate or saveamberparm ? and how did the transformation go on?

I'm pretty sure this happens at the solvate step, but why don't you just run
some experiments yourself and find out what happens? It should just be a
translation to the center of the box. Try working with a very simple solute
so that you can follow the transformations yourself.


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