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