AMBER Archive (2006)

Subject: RE: AMBER: Tutorial 2: Minimise and equlibrium error NaN

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jun 23 2006 - 06:28:17 CDT

Dear aa,

> NSTEP ENERGY RMS GMAX
> NAME NUMBER
> 1 NaN NaN 4.7181E+18 N
> 3812
>
> BOND = 515.5069 ANGLE = 2360.9706 DIHED
> = 5807.5212
> VDWAALS = ************* EEL = -42192.4813 EGB = NaN
> 1-4 VDW = 3537.6744 1-4 EEL = 23933.1851 RESTRAINT
> = 0.0000

Whenever you have a large VDW contribution it almost certainly means you
have two atoms either sitting on top of each other or very close. Leap does
not always spot these for various reasons. Note during minimisation at each
step the atom with the largest force on it is printed out. Here it is:

> NAME NUMBER
> 1 NaN NaN 4.7181E+18 N 3812

atom number 3812 which is a nitrogen. I would try visualizing your system to
see if you can see where the two atoms that clash are. You could start by
looking in the vicinity of atom 3812. Take a look in VMD (remember VMD
numbers from zero so this will be 3811 in VMD). Once you identify the
problematic atoms you should try and tweak your structure to remove these
clashes and then repeat the minimisation.

All the best
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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