AMBER Archive (2005)

Subject: AMBER: MD problems/shake

From: blakrose_at_gazeta.pl
Date: Mon Dec 19 2005 - 14:34:52 CST

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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