RE: AMBER: EEL and EAMBER values

From: Ross Walker <ross.rosswalker.co.uk>
Date: Wed, 2 Nov 2005 21:02:44 -0800

Dear Andrew,

> Could someone please tell me what EEL and EAMBER stand for in
> the following

EEL = electrostatic energy [q1*q2]/[4Pi*Eo*R^2]
EAMBER = The total energy from the amber force field equation. In this case
the sum of all the terms excluding the restraints. Subtract the restraint
energy from the total energy and you should get EAMBER.

> output, and can you tell me the implications of their not
> being a value under EEL and EAMBER.

Ah, but there is a value in your output... It is just lots of *'s. This
means that the value is too big to fit in the space allocated for it.

> 8021 -7.9708E+12 4.4444E+16 4.1793E+18 H2
> 5666
> BOND = 112235.6338 ANGLE = 433.8649 DIHED
> = 354.3798
> VDWAALS = 9487.9446 EEL = ************* HBOND
> = 0.0000
> 1-4 VDW = 182.8665 1-4 EEL = -264.4523 RESTRAINT
> = 6149.1888
> EAMBER = *************
> NMR restraints: Bond = 6149.189 Angle = 0.000 Torsion
> = 0.000

As you might guess these stars are very bad news and are often indicative of
errors in the starting structure. In this case your total energy is 10^12
KCal/Mol and even worse the RMS force is 10^16 KCal/Mol/A. This is a massive
force. Probably enough to accelerate one of your atoms to something
approaching the speed of light... If you look carefully at your output you
can see that the bond force is huge and the bond restraint force is
similarly large. Moreover the Electrostatic energy is so big it gets
replaced by *'s. This typically means that you have two atoms on top of each
other. Or an atom defined with an exceptionally high charge. The fact that
the VDW term is not huge suggests that the problem could be with the
hydrogen of a water molecule clashing with your solute. Since the hydrogens
of TIP3P water have no VDW radius. I would take a look at atom number 5666
H2 since this has the highest force on it and thus is probably closest to
the problem.

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross.rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.


-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Thu Nov 03 2005 - 05:53:00 PST
Custom Search