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,
Chris.
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Received on Tue Jan 06 2015 - 17:00:04 PST
