CABSdock issue: DSSP call failing

Question

[charlieclark1ee]

So, slightly niche but i figure there might be somebody with knowledge of either CABSDock or DSSP.

I've installed CABSDock, software for docking peptides to proteins, on an ubuntu HPC, following: https://bitbucket.org/lcbio/cabsdock/src/master/

CABSdock makes use of DSSP, a database of secondary structures for proteins. I installed DSSP following https://github.com/cmbi/hssp

However, when I direct CABSdock to the DSSP binary using --dssp-command PATH, I recieve the following error:

[CRITICAL] PDB: DSSP ERROR: mkhssp options: -h [ --help ] Display help message -i [ --input ] arg PDB ID or input PDB file (.pdb), mmCIF file (.cif/.mcif), or fasta file (.fa/.fasta), optionally compressed by gzip (.gz) or bzip2 (.bz2) -o [ --output ] arg Output file, optionally compressed by gzip (.gz) or bzip2 (.bz2). Use 'stdout' to output to screen -d [ --databank ] arg Databank to use (can be specified multiple times) -a [ --threads ] arg Number of threads (default is maximum) --min-length arg Minimal chain length (default = 25) --fragment-cutoff arg Minimal alignment length as fraction of chain length (default = 0.75) -O [ --gap-open ] arg Gap opening penalty (default is 30.0) -E [ --gap-extend ] arg Gap extension penalty (default is 2.0) --threshold arg Homology threshold adjustment (default = 0.05) -m [ --max- hits ] arg Maximum number of hits to include (default = 5000) -v [ --verbose ] Verbose mode --version Show version number and citation info

This 'error' message is just the -h output from the DSSP binary that is returned if you provide it with some sort of malformed call. Does anyone know what might be going on, or, failing that, how to see what CABSDock is calling DSSP with so I can debug further?

Answer 1

[Mensur Dlakic]

You are pointing to hssp binary. It should be to dssp binary:

https://github.com/cmbi/dssp