AMBER Archive (2006)

Subject: AMBER: NONB values adjusted?

From: Dave S Walker (dswalker_at_uoregon.edu)
Date: Tue Nov 28 2006 - 01:37:28 CST

Hello all,

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.

dsw
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