AMBER Archive (2003)

Subject: Protein - DNA complex simulation - protocol

From: Harikrishnan (harikrism_at_yahoo.co.in)
Date: Mon Apr 28 2003 - 23:40:39 CDT

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
accomplished'.

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.

thanks
Hari

________________________________________________________________________
Missed your favourite TV serial last night? Try the new, Yahoo! TV.
       visit http://in.tv.yahoo.com