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PostPosted: Wed Feb 06, 2013 6:16 pm 
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Millimolar User
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Joined: Wed Feb 06, 2013 6:13 pm
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Is there a command line interface to PMV or ADT to automate converting pdbqt to pdb and vice versa?

we are trying to use prepare_ligand.py ...

we tried to
set PYTHONHOME=/stuff/MGLTools-1.5.2/mgltools/lib/python2.5

and PYTHONPATH=/stuff/MGLTools-1.5.2/mgltools/MGLToolsPckgs:/stuff/MGLTools-1.5.2/mgltools/lib/python2.5/site-packages

but get a PyUnicodeUCS2 undefined symbol....

is there a preferred way to make python and numpy consistent?


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PostPosted: Wed Feb 13, 2013 6:00 pm 
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Joined: Fri Sep 21, 2012 3:25 am
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Location: Mexico
These are the lines I use to prepare my receptor:

/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py -r pdb.pdb -o pdb.pdbqt -A bonds_hydrogens -U nphs_lps_waters_nonstdres

and to prepare my ligands.

/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py -l ligand.mol2 -o ligand.pdbqt -A bonds -U nphs_lpsls

I hope this helps.


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