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

From: Nicolas Lux Fawzi <>
Date: Wed, 10 Oct 2007 09:03:09 -0700

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.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Oct 14 2007 - 06:07:10 PDT
Custom Search