AMBER Archive (2006)

Subject: Re: AMBER: NONB values adjusted?

From: Thomas Steinbrecher (
Date: Tue Nov 28 2006 - 10:31:33 CST

Dear Dave,

> I'm trying to understand better the NONB values r* (and e). From following
> the example on Van der Waals forces from the AMBER FAQs, it looks like the r*
> value for TIP3P water is 1.738, as shown in the parmfiles. From reading that
> example (as it pertained to Ca ion), to get the value of r*ij using only
> water molecules would be (2)(1.738)=3.476. This is close to the 3.166 value
> commonly shown as the 'sigma' value in the literature, and I'm wondering if
> there is some scaling factor that is missing, or are these parameters
> supposed to be different? Thanks in advance.

I think I ran across the same thing before, and here is what I think
might account for the difference: There are two common formulations of the
Lennard Jones Equation:

E = 4u * [ 1/4 (r0/r)^12 - 1/2 (r0/r)^6 ] (1)


E = 4e * [ (s/r)^12 - (s/r)^6 ] (2)

Here r0 and s (sigma) are two different parameters for the vdW distance,
r0 gives the minimum of the potential curve, s gives the point where E is
zero. They are connected by r0 = 2^(1/6)*s. amber specifies its parameters
according to (1) while most people normally think of (2) when they think
of vdW potentials. So if you multiply the literature (sigma) value by
~1.122, you obtain an (amber style) r0 of 3.553. While this is not exactly
what you report above, in my parm99.dat r0 for OW (water oxygen) is
1.7683. Also keep in mind that the designers of the amber force field
might (?) have modified the vdW radius for oxygen to take into account the
zero vdW radii on the water hydrogens.

Kind Regards,


Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA
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