AMBER: question on Lennard-Jones fitting in FF94 and 96

From: David Mobley <>
Date: Mon, 25 Sep 2006 10:07:45 -0700


I came across the following paragraph in the Advances in Protein
Chemistry review of molecular force fields from 2003 (by Ponder and
Case), and I wanted to confirm that this is correct, as several people
in the AMBER community have expressed surprise:

[Beginning with FF94...] "Once the charges and the''stiff'' internal
parameters for bonds and
angles were available (the latter estimated in the same way as outlined
above [from RESP HF 6-31G* fitting]), the Lennard-Jones parameters
could be established primarily by
reference to densities and heats of vaporization in liquid-state simulations.
Only a small number of sets of 6-12 parameters were necessary to achieve
reasonable agreement with experiment."

In particular: Is it really true that the LJ parameters were derived
AFTER charge fitting? (I just want to double-check this -- I'm writing
a paper in which I would say exactly this in the intro, and several
folks looking over a preprint thought I was wrong on this point).

As a follow up question, if this is the case, how is it that
Antechamber and GAFF seem to regard charges as "swappable", in the
sense that the same LJ parameters can be used with various different
charge models, or with the same atom type in various chemical
environments that will undoubtedly have different charges? Wouldn't
fitting of LJ parameters after charges imply that the two cannot be

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Received on Wed Sep 27 2006 - 06:07:13 PDT
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