Task #2658
Secondary structure assignment via DSSP as native gromacs code
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:
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 over 2 years ago
Gerrit received a related DRAFT patchset '2' for Issue #2658.
Uploader: Christian Blau (cblau@gwdg.de)
Change-Id: gromacs~master~Ia7b7bea83a6f82e2d38d1dcf1bd316516001b029
Gerrit URL: https://gerrit.gromacs.org/8458
#2 Updated by Alexey Shvetsov over 2 years ago
Hi!
Does someone already working on native dssp code?
#3 Updated by Mark Abraham over 2 years 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 over 2 years 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.