AMBER Archive (2009)

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

Date: Thu Jul 16 2009 - 04:01:15 CDT

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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