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Task #2658

Secondary structure assignment via DSSP as native gromacs code

Added by Christian Blau about 1 year ago. Updated about 1 year ago.

Status:
New
Priority:
Normal
Category:
analysis tools
Target version:
Difficulty:
simple
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Description

The GROMACS do_dssp analysis tool enables secondary structure analysis over a trajectory.

The tool, however depends on a call to the externally to be installed dssp tool, which is maintained here:

https://github.com/cmbi/xssp

User regularly complained about the challenge to get dssp set up correctly, and the main branch is currently broken from Ubuntu 18.04.
The current do_dssp implementation calls dssp and writes and parses back a dssp output file for every trajectory frame.

A GROMACS native dssp implementation will

  • greatly facilitate use of secondary structure assignment for trajectories, because it ships "out of the box" * speed up the analysis too, because no writing and reading of temporary files is needed * is a requirement for driving simulations to secondary structure targets, with a secondary structure assignment that can run in simulation time

The current xssp suite that includes dssp has a boost license that should allow the modification of their code for our purposes, however, okay from the software maintainers is still pending.

History

#1 Updated by Gerrit Code Review Bot about 1 year ago

Gerrit received a related DRAFT patchset '2' for Issue #2658.
Uploader: Christian Blau ()
Change-Id: gromacs~master~Ia7b7bea83a6f82e2d38d1dcf1bd316516001b029
Gerrit URL: https://gerrit.gromacs.org/8458

#2 Updated by Alexey Shvetsov about 1 year ago

Hi!

Does someone already working on native dssp code?

#3 Updated by Mark Abraham about 1 year ago

Yes, Christian has a draft of an import of xssp. If you're interested to collaborate, I'm sure he'd consdier tagging you on gerrit.

#4 Updated by Christian Blau about 1 year ago

Mark Abraham wrote:

Yes, Christian has a draft of an import of xssp. If you're interested to collaborate, I'm sure he'd consdier tagging you on gerrit.

Tagged Alexey Shvetsov in gerrit draft.

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