AMBER Archive (2005)

Subject: Re: AMBER: coordinated water molecules deleted when addions

From: David A. Case (case_at_scripps.edu)
Date: Mon Aug 01 2005 - 08:39:39 CDT

On Mon, Aug 01, 2005, Ye Mei wrote:
>
> There are four water molecules coordinated to MG2+ ion in my peptide.pdb
> file. Then I combine it with ligand and solvate them in TIP3PBOX. Everything
> is fine here. But when I add Cl- ions to neutralise this complex, I
> noticed that one of the coordinated water molecules has been deleted and
> replaced by Cl-. The coordinated water molecules are very important in this
> system. How can I add ions to it but keep the coordinated water molecules?

You might have to add Ions by hand; or you could "trick" the system by naming
the waters that are coordinated to the ion to something different. Then the
addIons command won't consider them for removal. If you play around a little
bit you should be able to get this to work.

...good luck...dac

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