AMBER Archive (2006)

Subject: Re: [UCE]AMBER: (no subject)

From: Thomas Cheatham (
Date: Sun Jul 09 2006 - 18:18:49 CDT

> I get the following error on occasions when I am doing a dynamics run. I have
> read the previous posts for this error, but I am not sure exactly which values
> in ew_legal.h to change so I can perform the run with a cut off 9 angstroms or
> greater.
> parameter skinnb+cutoffnb: (nonbond list cut) has value 0.11000E+02
> This is outside the legal range
> Lower limit: 0.00000E+00 Upper limit: 0.10272E+02

AMBER can only do minimum image conventions; what this means is that you
cannot have two distinct images of the same atom within the cutoff.
According to the message, that largest cutoff for the pairlist build is
10.2 angstroms. With a 9A cutoff and a 2A buffer or skin, this is 11A and
is greater than the 10.2A. [Likely you have a box that is fairly small,
something like ~20.4 angstroms on a side if cubic].

There is nothing in ew_legal.h that can be changed to overcome this.

To run a 9A cutoff, you can set SKINNB=1.0 (in the &ewald namelist).
Otherwise, if you want to run with a larger buffer or "skin" beyond the
9A cutoff, you will need to create a larger box.

\-/ 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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to