[AMBER] Undocumented DSSP commands and torsional analysis

From: Eugene Yedvabny <eyedvabny.berkeley.edu>
Date: Tue, 26 Aug 2014 00:48:53 -0700

Hello Amber Community,

I am trying investigate the secondary structure of a short disordered
peptide using cpptraj's secstruct command. I am running into some
complications and was hoping somebody would be kind enough to shed some
light and/or suggest alternatives:

1) The newest manual lists 6 different ss types detected by DSSP algorithm,
but looking at the source code, there is support for the 7th 'Bend' type.
In my secstruct outputs I don't see a '7' type in either the raw or the
averaged outputs. Can I then assume I have no bends in the peptide, or is
that code still experimental and perhaps not reliable?

2) Is there any way to parse the *type* of a Turn across a group of
residues? For example, secstruct stats show a Turn on residues 6, 7 and 8,
which suggests an alpha-turn 5-9. But the h-bond analysis reveals that
there's a mixture of 5-8 and 6-9 turns in addition to 5-9 in the ensemble.
Is there a way to refine reported 'T' into 'T4', 'T5', or 'T6' for the
different lengths of turns short of modifying the source?

3) DSSP is intrinsically based off h-bonds. Is there any algorithm in
cpptraj that would perform a comparable analysis on the basis of dihedral
angles? I am trying to detect if there are any non-h-bond-stabilized
structural motifs in the peptide.

Thank you,
Eugene Yedvabny
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Received on Tue Aug 26 2014 - 01:00:02 PDT
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