AMBER Archive (2009)

Subject: 答复: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished,

From: Zhongjie Liang (
Date: Thu Jul 16 2009 - 04:16:02 CDT

Dear Dr. Thomas Steinbrecher,
     Thanks for the suggestion. I checked the atoms involved, but found that
the atoms were in the same one small molecule, and the small molecule was
restrained at first dynamics. It looks like that it is not their problem. Is
there a possible that some else has the question?
     Best regards.
                              Zhongjie Liang

发件人: [] 代表
发送时间: 2009年7月16日 17:01
收件人: AMBER Mailing List
主题: Re: [AMBER] Coordinate resetting (SHAKE) cannot be accomplished,

Hi Zhongjie,

> I got a protein structure by homology modeling, but when I do the
> molecular dynamics by AMBER, I got the warning message as follows:

You should mention what kind of MD protocoll you follow, homology modelled
structures can contain bad initial contacts that need to be carefully
equilibrated away. Do you minimize your structure first? Equilibrate to
the desired temperature with light restraints?

> Coordinate resetting (SHAKE) cannot be accomplished,
> deviation is too large
> NITER, NIT, LL, I and J are : 0 2 2103 4164 4165

The last two numbers give you the atom numbers involved. Look at this part
of your structure and check if anything looks strange. In the worst case,
run a (short) MD printing the coordinates every step and check what
exactly causes your system to crash...

Kind Regards,


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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