AMBER Archive (2005)

Subject: AMBER: MD problems (SHAKE)

From: blakrose_at_gazeta.pl
Date: Mon Dec 19 2005 - 06:49:41 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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