> myself. What I can tell you for the moment is that OPLS, in fact a
> historical derivative of Amber which has long since grown into its own
A minor point of clarification, and DAC or Merz can correct me if I am
wrong, but I think AMBER adopted the OPLS approach, not the other way
around. The key here is not the intramolecular (which were similar or
shared in both cases), but the intermolecular terms and the use of liquid
phase simulations to fit vdw parameters to reproduce density. The
approaches started to differentiate when AMBER realized the electrostatic
potential charge fitting for the charges (as opposed to empirical charge
or QM-interaction energy charge fitting which occured prior to the OPLS
liquid density matching ideas) was a potentially better, but not
sufficient approach. They needed balance and hence adopted the OPLS idea
of vdw from neat liquid simulations. From the classic 1995 Cornell et al.
parm94 paper: "We have been influenced by the OPLS philosophy of balanced
solvent-solvent and solute-solvent interactions in our thoughts about a
second-generation force field..."
As an aside, it is interesting to go back to Jorgenson's 1988 article
where quotes like the following appear: "Computer simulations are
undoubtedly destined to become an increasingly important means for
investigating the structures and dynamics of biological systems" and
"There is little doubt that there will be a continual evolution in force
fields with added complexity and improved performance". Wow! So much has
improved *yet*, so much has stayed the same.
I am reinvigorated reading these papers again. Those of you new to the
field and/or those who *haven't* read the earlier papers should take the
time to read and understand these earlier force field papers... This is a
better use of time than blindly applying MM-GBSA calculations.
--tec3
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Received on Fri Mar 11 2016 - 20:00:03 PST
