AMBER Archive (2006)

Subject: AMBER: ff99SB vs ff02 (ff02pol.rl)

From: Nicolas Lux Fawzi (fawzin_at_berkeley.edu)
Date: Mon Oct 30 2006 - 19:48:32 CST

If I understand correctly, Amber's ff99 has been improved (creating
ff99SB) by changing the backbone dihedrals, correctly taking into
account both phi and psi as well as phi' and psi', fitting to some QM
derived values as well as checking populations of different di- and
tetra-peptide minima in classical explicit water simulations.

My question is: has the ff02pol.rl addressed the same backbone dihedral
"problems" that ff99SB has addressed, or is the ff02pol.rl still likely
to need similar revision? It is difficult to compare the percentages
of secondary structures from Hornak et al Proteins 2006 (65:712-725)
and Wang et al. JCompChem 2005 since the peptides for population
determination are different (ace-ala[7]-nme vs. ala[3] ?)

My application is to study a solvated peptide in explicit water and
have settled on testing ff99SB with TIP3P but would like to try a
polarizable comparison. Would ff02pol.rl with POL3 provide a
reasonable comparison?

Thanks for any perspectives you might have.

-Nick

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