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

From: David A Case <case.biomaps.rutgers.edu>
Date: Mon, 22 Dec 2014 08:36:27 -0500

On Mon, Dec 15, 2014, nealec wrote:
>
> I am confused as to why the Amber force field does not seem to apply a
> psi dihedral angle to the N-terminal residue of a protein when using a
> charged N-terminus (nitrogen type N3).

I'm guessing that there is little experimental evidence about psi propensities
for N-terminal residues. Quantum calculations might help, but I don't think
this problem has been attacked in any coordinated way, so Amber force fields
are giving a "default" psi behavior there.

Comments are welcome in case I am missing something.

...dac


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Received on Mon Dec 22 2014 - 06:00:05 PST
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