AMBER Archive (2008)

Subject: AMBER: potassium ion

From: Lars Skjærven (
Date: Thu May 22 2008 - 08:09:59 CDT

Dear Amber users,
I'm doing a simulation of a protein with a potassium which is
suggested by several experimental studies to be bound to certain
residues in the active site. After equilibration, the potassium seems
correctly located between to oxygen atoms of two amino acids. After
~500ps of "production" with no restraints, and 1fs time-step, the ion
starts flying around in the binding site, and eventually it jumps out
in the solution.

1. Can I trust the potassium parameters that follows ff03?
2. Do you have any hints on how I can interpret this behaviour?

I did a similar simulation, however with MgATP bound. Here, the Mg ion
stays bound to the ATP and the protein.

Thanks in advance :-)

Lars Skjaerven
University of Bergen, Norway
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