normal Error with DSSP while going through the small molecule binding tutorial

  • hawo
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3 years 6 months ago #8777 by hawo
Hello everyone. I seem to have trouble running this tutorial (specifically step 1B): cgmartini.nl/index.php/martini-3-tutoria...all-molecule-binding

I've downloaded Martini 3, and I got DSSP 2.3.0 from this repo that the CMBI website refers to. The command I'm trying to run looks like this:
./martinize -f 181L.pdb -ff martini303v.partition -x CG.pdb -o topol.top -dssp full-path-to-dssp-dir/mkdssp -elastic

And the output I get is this:
A
B
C
D
E
INFO       If you use this script please cite:
INFO       de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
INFO       Chain termini will be charged
INFO       Residues at chain brakes will not be charged
INFO       The None forcefield will be used.
INFO       Local elastic bonds will be used for extended regions.
INFO       Read input structure from file.
INFO       Input structure is a PDB file.
INFO       Found 3 chains:
INFO          1:   A (Protein), 1289 atoms in 162 residues.
INFO          2:   A (Unknown), 16 atoms in 4 residues.
INFO          3:   A (Water), 136 atoms in 136 residues.
INFO       Removing HETATM chain A consisting of 4 residues.
INFO       Removing 136 water molecules (chain A).
INFO       Total size of the system: 162 residues.
Traceback (most recent call last):
  File "/usr/lib/python2.7/runpy.py", line 174, in _run_module_as_main
    "__main__", fname, loader, pkg_name)
  File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
    exec code in run_globals
  File "./martinize/__main__.py", line 10, in <module>
  File "./martinize/martinize/cli.py", line 204, in main
  File "./martinize/martinize/core.py", line 546, in main
  File "./martinize/martinize/core.py", line 252, in read_input_file
  File "./martinize/martinize/core.py", line 143, in determine_secondary_structure
  File "./martinize/martinize/IO.py", line 619, in dss
  File "./martinize/martinize/secstruc.py", line 198, in call_dssp
IOError: [Errno 2] No such file or directory: 'chain_A.ssd'

The problem seems to be specifically with DSSP (as indicated by the second to last line). However, the mkdssp executable seems to be working fine if I call it separately on the same PDB file, successfully producing a PDB with a secondary structure. Should I get another DSSP distribution, or am I calling it wrong, or is the problem caused by something else?

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  • hawo
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3 years 6 months ago - 3 years 6 months ago #8778 by hawo
Never mind, I should've read the forum more carefully. I downloaded a DSSP executable from here as suggested in this thread and it worked. I'm sorry.
Last edit: 3 years 6 months ago by hawo.

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3 years 6 months ago #8779 by riccardo
Thanks for following up on your own question with the solution!

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3 years 1 month ago #8939 by Serrano
Unfortunately, the link to the executable file does not work anymore. I compiled DSSP from the official repo . But I got the same "IOError: [Errno 2] No such file or directory: 'chain_A.ssd'". So I finally ended up installing DSSP from apt-get via
sudo apt-get install dssp
and it worked at once.

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3 years 1 month ago #8940 by riccardo
Thanks for the note!
I'll make a note that we should point to this thread from the tutorial in case of problems with DSSP.

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2 years 10 months ago #9089 by jessicab
I also had the same issue with dssp/mkdssp. I had built it from source and it was correctly installed.

On using the conda insallation it worked without a problem-
conda install -c salilab dssp

-Jessica

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