AMBER Archive (2007)

Subject: AMBER: ff99SB and the N- and C- charged terminal residues

From: Nicolas Lux Fawzi (fawzin_at_berkeley.edu)
Date: Wed Oct 10 2007 - 11:03:09 CDT

I am using ff99SB for a number of studies of systems with charged
terminal residues (as opposed to acteyl and N-methylamine groups) and I
think I've noticed that the ff99SB dihedral are not being used for the
1st psi angle and the last phi angle in the peptide chain. For a two
amino acid (single peptide bond) zwitterionic system, this would be the
only psi and phi angles.
Could you tell me what ff is being applied (I know I can look at the
prmtop to find out, but I can't answer this next question ...) and what
rationale is used for choosing the dihedral parameters for charged
terminal amino acids. I couldn't see anything about this in the paper
describing ff99SB.
Thanks!
-Nick
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