AMBER Archive (2009)

Subject: [AMBER] clarification DNA forcefield

From: Taufik Al-Sarraj (taufik.alsarraj_at_utoronto.ca)
Date: Thu Dec 03 2009 - 22:01:02 CST

Hello,
I have been using ff99SB and ff99bsc0 to model DNA in solution and i
noticed some articles (Babin, 06) stating that ff02 (with polarizable
forcefield) is better at describing DNA in solution, especially in long
simulations. However, (In Suk Joung, 09) still uses ff99SB and ff99bsc0.
in (Perez 07) i could not find any reference to polarization in bsc0
only corrections to back bone torsions.

Does this mean my simulations of DNA in explicit water using ff99SB and
ff99bsc0 are correct, but if i choose to use implicit solvents i should
use ff02?

lastly, what is the recommended cutoff for non-bound interactions for
DNA in explicit solvents? i thought 12A for LJ and 8A for PME were
sufficient.

Thanks,
Taufik

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