unanswered Martinize dssp "The system cannot find the path specified"

  • p.albanese
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3 years 2 months ago #8812 by p.albanese
Hi,

I'm trying to run the script, but the exe of dssp is not picked up. I tried both dssp-3.0.0-win32 and dssp-2.0.4-win32.

This is the command:

python martinize.py -f mod13_s_dim_ren.pdb -o 13_s_dim.top -x 13_s_cg.pdb -dssp C:\Users\alban001\Desktop\martini_cg\dssp-3.0.0-win32.exe -p backbone -ff martini22

This the error I get out:

The system cannot find the path specified.
Traceback (most recent call last):
File "martinize.py", line 4805, in <module>
main(options)
File "martinize.py", line 4493, in main
ss += chain.dss(method, executable)
File "martinize.py", line 3302, in dss
self.set_ss(ssDetermination[method](self, atomlist, executable), source=method)
File "martinize.py", line 2663, in call_dssp
if atom[0][0] != 'H' and atom[0][:2] != 'O2': p.stdin.write(pdbOut(atom).encode('utf-8'))


If I remove the -dssp flag the script run smoothly and gives all the outputs.


Any idea ?


Thanks,
Pascal

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