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Error with DSSP while going through the small molecule binding tutorial
- hawo
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3 years 4 months ago #8777
by hawo
Error with DSSP while going through the small molecule binding tutorial was created 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:
And the output I get is this:
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?
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 4 months ago - 3 years 4 months ago #8778
by hawo
Replied by hawo on topic Error with DSSP while going through the small molecule binding tutorial
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 4 months ago by hawo.
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- riccardo
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3 years 4 months ago #8779
by riccardo
Replied by riccardo on topic Error with DSSP while going through the small molecule binding tutorial
Thanks for following up on your own question with the solution!
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- Serrano
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2 years 11 months ago #8939
by Serrano
Replied by Serrano on topic Error with DSSP while going through the small molecule binding tutorial
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 viaand it worked at once.
sudo apt-get install dssp
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- riccardo
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2 years 11 months ago #8940
by riccardo
Replied by riccardo on topic Error with DSSP while going through the small molecule binding tutorial
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.
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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- jessicab
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2 years 8 months ago #9089
by jessicab
Replied by jessicab on topic Error with DSSP while going through the small molecule binding tutorial
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-
-Jessica
On using the conda insallation it worked without a problem-
conda install -c salilab dssp
-Jessica
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