AMBER Archive (2008)

Subject: Re: AMBER: bond breaking in proteins

From: David A. Case (
Date: Tue Feb 26 2008 - 18:41:26 CST

On Tue, Feb 26, 2008, Eddie Mende wrote:

> Thanks for the help Dr. Case and Dr. Seabra,
> it was not possible for me to upload the whole protein in pdb form.
> The protein is 85 amino acid residues, and the phospate group
> is attached to a histidine....Implicit solvation simulations
> are supposed to be held at 1 atm pressure, right?.

It sounds like your problem may have little to do with waters, or anything
like that. Have you examined what happens with a pure QM model of a single
phospho-histidine residue? I would suggest making sure that everything is
fine for a single residue before worrying about fine details (especially if
bonds are spontaneously breaking).


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