[AMBER] Recent Enhancements to secstruct/dssp in Cpptraj

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Fri, 6 Sep 2019 15:47:12 -0400

Hi All,

Just wanted to make you aware of some recent enhancements that have
been made to the secstruct/dssp action in GitHub (not AmberTools 19)
cpptraj. Since there are some changes in how things are calculated,
results will differ somewhat from those previously obtained.

The secondary structure assignment now matches the original paper
exactly, i.e. extended beta (E) and isolated beta bridge (B) is
assigned instead of parallel/anti-parallel beta. I had initially
written it to output parallel/anti-parallel because that's the way it
was originally implemented in ptraj and I wanted to keep backwards
compatibility. However, I think it makes more sense to use the
original definitions if for no other reason than a residue in a strand
could be potentially both parallel and anti-parallel. The original
behavior can be restored via a new keyword, 'betadetail'.

The new code is actually faster to assign secondary structure than the
original code (although the bottleneck is still hydrogen bond
calculation), and uses way less memory. The helix assignment code is
much more robust as well, and isolated stretches which used to be
labeled as a helix are now correctly labeled as turn. Also, beta bulge
structure is now identified and correctly assigned extended in
accordance with the original definition.

The associated pull request for those interested is here.



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Received on Fri Sep 06 2019 - 13:00:02 PDT
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