[Dock-fans] Error with molconvert

Munoz.Ines imunoz at cnio.es
Sun Sep 13 12:42:13 PDT 2015


Dear all,
Following the tutorial of this link (http://wiki.docking.org/index.php/DOCKovalent_3.7), when executing 
$DOCKBASE/ligand/generate/build_smiles_ligand.sh lig.smi --covalent
and using the ligand that you have in the web
COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO

Could you please help me to find what's wrong? By the way, when I remove the brackets, cannot find another file.
Thanks in advance.
Regards,
Inés.


$ echo "COC(=O)C(C#N)C([SiH3])c3c(c1ccc(C)cc1)c2c(N)ncnc2n3CCCO xtal-lig" | $DOCKBASE/ligand/protonate/prot_marvin.py -H 7.4 -d 20 -o outfile
Traceback (most recent call last):
  File "/home/ines/Software/DOCK-3.7-beta2.0.1/ligand/protonate/prot_marvin.py", line 156, in <module>
    sys.exit(main(sys.argv))
  File "/home/ines/Software/DOCK-3.7-beta2.0.1/ligand/protonate/prot_marvin.py", line 152, in main
    threshold=options.threshold)
  File "/home/ines/Software/DOCK-3.7-beta2.0.1/ligand/protonate/prot_marvin.py", line 126, in run_cxcalc
    for compound in accepted:
  File "/home/ines/Software/DOCK-3.7-beta2.0.1/ligand/protonate/prot_marvin.py", line 124, in <genexpr>
    accepted = (sub for sub in calculated if sub[2] > threshold)
  File "/home/ines/Software/DOCK-3.7-beta2.0.1/ligand/protonate/prot_marvin.py", line 106, in cxcalc_single
    for taut_smiles, taut_dist in tautomers:
  File "/home/ines/Software/DOCK-3.7-beta2.0.1/ligand/protonate/prot_marvin.py", line 85, in generate_tautomers
    for smiles, dist in processed:
  File "/home/ines/Software/DOCK-3.7-beta2.0.1/ligand/protonate/prot_marvin.py", line 69, in _process_cxcalc_distribution_results
    for result in results:
  File "/home/ines/Software/DOCK-3.7-beta2.0.1/ligand/protonate/prot_marvin.py", line 67, in <genexpr>
    results = (line.split() for line in results \
  File "/usr/local/lib/python2.7/dist-packages/sh.py", line 565, in next
    self.wait()
  File "/usr/local/lib/python2.7/dist-packages/sh.py", line 500, in wait
    self.handle_command_exit_code(exit_code)
  File "/usr/local/lib/python2.7/dist-packages/sh.py", line 516, in handle_command_exit_code
    raise exc(self.ran, self.process.stdout, self.process.stderr)
sh.ErrorReturnCode_1:

  RAN: '/home/ines/Software/ChemAxon/MarvinBeans/bin/molconvert smiles -T dist'

  STDOUT:
#SMILES    dist


  STDERR:
 error: Cannot recognize format ([]?)
Unrecognized file contents:
dominanttautomerdistribution:FAILED...


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