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PostPosted: Mon Feb 18, 2013 10:43 am 
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Joined: Mon Feb 18, 2013 9:57 am
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Dear all,
I am unable to convert the following molecule (C1=CC=CC3=C1C2=NN=C(C)[N]2N=C3, 3-methyl-[1,2,4]triazolo[3,4-a]phthalazine) into a correct pdbqt file from whatever file format available on ChemBioDraw.
I tried Autodock and also Babel programmes
the conversion into pdbqt generates new incorrect bonds between the two opposite carbons of the triazolo ring and protonates the two close nitroges of the triazolo ring as well. this is aboslutely incorrect, given the original structure of the molecule.
any suggestions would be much appreciated.
thanks to all,
Best regards,
Nicola


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