[AMBER] Missing psi dihedral at cationic N-terminus of protein/peptide?

From: nealec <nealec.rpi.edu>
Date: Tue, 06 Jan 2015 19:54:01 -0500

Dear David and Carlos:

If it is the case that an N-terminal psi is intentionally omitted due to
lack of data, then why include the C-terminal phi?

C -N -CT-C 1 0.850 180.000 -2.
C -N -CT-C 1 0.800 0.000 1.

It seems inconsistent to me. Not to say that it couldn't work, but the
simplest explanation for including a C-terminal phi (no name change in
the terminal carbon type) and not including an N-terminal psi (has a
name change in the terminal nitrogen type) is that the N to N3
difference was simply forgotten.

Also, Carlos, sorry for my poor description earlier. I was not
suggesting to simply use the non-N-terminal version of the N-terminal
amino acid on its own. Rather, I was noting that if I cap the peptide's
N-terminus with an acetyl group, then I get the regular "N" atom type
back (rather than "N3") and thus I also get the psi dihedral back.

This could be important for people studying the effect of capping on a
peptide, since the difference is (a) the cap (b) changes in charges and,
perhaps unexpectedly (c) the omission of some psi dihedral terms.

Thank you,

AMBER mailing list
Received on Tue Jan 06 2015 - 17:00:04 PST
Custom Search