AMBER Archive (2005)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Aug 01 2005 - 12:09:17 CDT

Dear Ye Mei,

> 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?

The addions command will add the ions at regions of high potential,
replacing and overlapping water molecules. If you need to keep the four
coordinated water molecules then I would trick Leap into thinking these are
not actually solvent water molecules. You can do this by renaming the
coordinated water molecules as something like CWT, or some other unused
residue name. Then create a new residue in Leap based on TIP3P water:

CWT = copy WAT

You can then load everything as you did before and when you add the ions
Leap should avoid replacing any of the CWT waters.

I hope this helps.
All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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