atom types differ for the charged termini (eg N3 for the nitrogen).
since the charges and types differ, in principle different dihedral
terms should be applied. We didn't do fitting for those, only the blocked
residues. One could apply 99SB to the charged termini too, but I did not
set it as the default since 1) we technically didn't develop modifications
for that and 2) termini are quite often flexible anyway.
Carlos
On 10/10/07, Nicolas Lux Fawzi <fawzin.berkeley.edu> wrote:
> 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
>
-----------------------------------------------------------------------
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 - 06:07:11 PDT
