AMBER Archive (2004)

Subject: Re: AMBER: NMR restraints-Floating point exception

From: David A. Case (
Date: Wed Feb 25 2004 - 10:17:46 CST

On Wed, Feb 25, 2004, John wrote:
> I want to use some NMR restraints in a simulation. The same simulation
> without the restraints runs fine. I followed the Refinement of a DNA Duplex
> tutorial to prepare the restraint file (distance and torsion angle
> restraints). When I introduce the restraints I get the following message:
> [1]+ Floating point exception/usr/local/amber7/exe/sander -O -i...
> &cntrl
> imin=0, ntx=1, nmropt=1, ipnlty=1, pencut=-0.001,
> ntwr=1000, ntwx=200,
> ntf=2, ntb=2, cut=12.0, ibelly=0,
> nstlim=80000, dt=0.001,
> temp0=298.0, tempi=0.0, ntt=1,
> ntp=1, taup=2.0, npscal=1,
> ntc=2,
> &end

Try running 10 steps with ntpr=1; that will give you more information.

You are trying to do a constant pressure simulation, starting at 0K. This
is very dangerous. It could be that you were lucky without restraints, and
hit a common error with them. Use LISTIN=POUT to make sure that your
restraints are OK.

> Number of triangulated 3-point waters found: 0

It also looks like you are trying to do a constant pressure and/or
periodic boundary condition simulation with no water(?). That will never

....good luck...dac


================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to