Re: AMBER: MD problems/shake

From: Thomas E. Cheatham, III <>
Date: Mon, 19 Dec 2005 13:53:40 -0700 (Mountain Standard Time)

> 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
> 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.

This SHAKE issue comes up often, and it usually results from either
instabilities in the system (such as atoms too close together as can be
checked by running the checkoverlap command in ptraj) or other artifacts
(such as force constants that are too large, atoms with zero van der Waals
within another atoms vdw radii, etc) that lead to large forces, hence
large movements, which stress the integrator or SHAKE to their failing
point. This is discussed in the AMBER e-mail archives and on the AMBER
WWW page in great detail. However, as so many hits come up when I search
and since it is the holiday season, I felt like summarizing again...

IF this is occurring in the ligand-- and it looks OK-- perhaps you have
force constants for the bonds that are too large? How did you get the
parameters for your ligand and can you run the ligand alone (without
water but with SHAKE on)? If you can run the isolated ligand, make sure
minimization of the entire complex was done prior to MD and that there are
no overlapping atoms (which may not be visible when you view the

You can follow up with more specific questions to me if need be.

\-/ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy
-/- Departments of Med. Chem. and of Pharmaceutics and Pharm. Chem.
/-\ Adjunct Asst Prof of Bioeng.; Center for High Performance Computing
\-/ University of Utah, 30 S 2000 E, SH 201, Salt Lake City, UT 84112
/-\ (801) 587-9652; FAX: (801) 585-9119
\-/ BPRP295A

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Received on Mon Dec 19 2005 - 21:53:01 PST
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