AMBER: MD problems (SHAKE)

From: <>
Date: Mon, 19 Dec 2005 13:49:41 +0100 (CET)

Dear Amber users!
I have a problem with MD. I am doing dynamics on ligand-protein
complex in water. During my MD (527ps) a got a message:
Coordinate resetting (SHAKE) cannot be accomplished,
     deviation is too large
     NITER, NIT, LL, I and J are : 0 1 2089 4153 4154
     Note: This is usually a symptom of some deeper
     problem with the energetics of the system
Are I and J atoms number?
I have tried to increase box, but the problem remains.
I looked at the structure using VMD. If 4153 and 4154 are
problematic atoms numer than this is a ligand problem, but it
seems perfectly ok.
Please help me.
|awel Gruszczynski
Gdansk Uniwersity POLAND
Chemistry Departament

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Received on Mon Dec 19 2005 - 12:53:01 PST
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