Re: [AMBER] nocut MD SHAKE error

From: Anupam Goel <>
Date: Tue, 6 Jan 2015 21:19:00 +0000

Longer minimization step solved the problem, much thanks to Daniel and David for help !
From: Daniel Roe []
Sent: Monday, January 05, 2015 4:31 PM
To: AMBER Mailing List
Subject: Re: [AMBER] nocut MD SHAKE error


On Mon, Jan 5, 2015 at 2:14 PM, Anupam Goel <> wrote:
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> Can you suggest which deviation is being talked about in the error?

The usual cause for this kind of SHAKE problem with implicit solvent
is the system has not been properly minimized beforehand. Make sure
you have run enough minimization before trying MD. There are also
several other causes for this (such as a bad atomic overlap in your
system somewhere). Googling the phrase "coordinate resetting (shake)
cannot be accomplished, deviation is too large" provides many useful
hints on how to fix this issue.

Hope this helps,


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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue Jan 06 2015 - 13:30:02 PST
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