From: Ross Walker <>
Date: Tue, 1 Mar 2005 08:46:08 -0800

Dear Ilaria,
NaN essentially means Not a Number or infinity. It is generally generated by
dividing by zero. The source of this problem is the *****'s. When sander
cannot fit a number in the output space provided it instead prints *****'s
typically you should never see this as the output spaces have been chosen to
match the sizes of numbers expected from a simulation. Thus the ****'s mean
something is seriously wrong. The problem in your case is with your
restraints. The restraint energy is huge which is leading to a massive
potential energy and therefore a massive temperature. I would check your
restraint definitions carefully before running more simulations.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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From: [] On Behalf Of
ilaria massarelli
Sent: 01 March 2005 00:45
Subject: AMBER: NaNQ

Good morning,
I had some problems with sander. In some runs of MD of a protein-ligand
complex I obtained the label -NaNQ and a lot of ******** for several terms
during the sander run. I report here an example. This is a fragment of a 15
ps equilibration at 300 K performed after an heating of 5 ps from 0 to 300K.
NSTEP = 14500 TIME(PS) = 19.500 TEMP(K) =********* PRESS = 0.0
 Etot = -NaNQ EKtot = ************ EPtot = -NaNQ
 BOND = 734.0641 ANGLE = 1856.5024 DIHED = 2728.0707
 1-4 NB = 924.8968 1-4 EEL = 13059.3943 VDWAALS = -2205.6991
 EELEC = -17879.4424 EGB = -NaNQ RESTRAINT = ************
 ESURF = 51.0843
 EAMBER (non-restraint) = -NaNQ

What do they mean? And how can I solve this problem?
thank you
Ilaria Massarelli


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Received on Tue Mar 01 2005 - 16:53:00 PST
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