AMBER Archive (2006)

Subject: AMBER: Simulating a periodic crystal

From: Jiang Jianwen (
Date: Wed Mar 29 2006 - 09:01:26 CST

Dear Amber Users,

I am trying to use Amber8 to run simulation in a periodic protein or DNA
crystal structure. Part of the biomolecule is outside of the unit cell
or simulation box, in other words, there are covalent bonds between
atoms in different unit cells.

I did some search in the Amber website and found some information with
regard to this issue (in the attached files) Dr. David A. Case said
"only non-covalent interactions between unit cells are allowed", to my
understanding, this implies that Amber will not work for my case.
However, from Dr. Thomas E. Cheatham, III's comments and several of Dr.
T. A. Darden's papers [(Biophys. J. 78, 668 (2000), Biochemistry, 32,
1443(1993)], it seems Amber can do simulation in a periodic crystalline
environment even part of a biomolecule crosses the unit cell boundary.

Could anyone give some hints and clarify on this issue? Thanks



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