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installation of covalent dock in linux mint 18
http://mgl.scripps.edu/forum/viewtopic.php?f=11&t=3328
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Author:  violetmary [ Tue Oct 25, 2016 2:12 pm ]
Post subject:  installation of covalent dock in linux mint 18

oem@viji ~ $ su
Password:
viji oem # cd /usr/local/adcovalent/
viji adcovalent # ls
3upo_protein.pdb ligand.mol2 pythonsh residues.log
CopyMol.py ligcovalent.pdb ResidueProfiler.py
CopyMol.pyc prepareCovalent.py ResidueProfiler.pyc
viji adcovalent # python /prepareCovalent.py --ligand ligand.mol2 \> --ligindices 1,2\
> --receptor 3upo_protein.pdb\
> --residue B:SER222\
> --outputfile ligcovalent.pdb
python: can't open file '/prepareCovalent.py': [Errno 2] No such file or directory
viji adcovalent # python prepareCovalent.py --ligand ligand.mol2 --ligindices 1,2 --receptor 3upo_protein.pdb --residue B:SER222 --outputfile ligcovalent.pdb
Processing residue B:SER222
[start] output filename is: ligcovalent.pdb
prepareCovalent.py:76: FutureWarning: comparison to `None` will result in an elementwise object comparison in the future.
if not p2 == None:
CHAIN B
Writing output filename: ligcovalent.pdb
viji adcovalent # cd /usr/local/MGLTools-1.5.6/bin/
viji bin # > py
pydoc python2.5 python-config
python python2.5-config pythonsh
viji bin # > py
pydoc python2.5 python-config
python python2.5-config pythonsh
viji bin # > pythonsh
viji bin # /usr/local/MGLTools-1.5.6/bin/pythonsh
viji bin # /usr/local/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r 3upo_protein.pdb -A hydrogens
/usr/bin/env: ‘/home/oem/MGLTools-1.5.6/bin/pythonsh’: No such file or directory
viji bin # /usr/local/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r3upo_protein.pdb -A hydrogens
/usr/bin/env: ‘/home/oem/MGLTools-1.5.6/bin/pythonsh’: No such file or directory
viji bin # /usr/local/MGLTools-1.5.6/bin/pythonsh
viji bin # /usr/local/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r 3upo_protein.pdb -A hydrogens
/usr/bin/env: ‘/home/oem/MGLTools-1.5.6/bin/pythonsh’: No such file or directory
viji bin # su root
viji bin # /usr/local/MGLTools-1.5.6/bin/pythonsh
viji bin # /usr/local/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r 3upo_protein.pdb -A hydrogens
/usr/bin/env: ‘/home/oem/MGLTools-1.5.6/bin/pythonsh’: No such file or directory
viji bin # /usr/local/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r 3upo_protein.pdb -A hydrogens
viji bin # /usr/local/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r 3upo_protein.pdb -A hydrogens
viji bin # /usr/local/MGLTools-1.5.6/bin/pythonsh
viji bin # /usr/local/MGLTools-1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r ligcovalent.pdb
viji bin #

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