Protein - DNA complex simulation - protocol

From: Harikrishnan <>
Date: Tue, 29 Apr 2003 05:40:39 +0100 (BST)

Dear sir,

I've started using Amber recently. I'm trying to do a
protein-dna complex simulation with ions and water.
When I start the dynamics after minimization, the
water molecules are seen escaping and the box shape
changes. After about 300 ps simulation, it stopped
with error saying 'coordinate resetting cannot be

I feel that there is some problem with my
equilibration protocol. Can anybody suggest me the
steps to be followed for a DNA-protein complex
simulation? Any pointer to papers describing the
protocol also would be of great help.


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Received on Tue Apr 29 2003 - 05:53:00 PDT
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