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PostPosted: Thu Jun 13, 2013 3:13 pm 
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I have a molecule with 3 rings. Two of the rings are fused. I have a pdb file that looks fine in ChemDraw 3D and in ADT. If I save it as a pdbqt file in ADT and then open up it, one of the bonds in one of the rings that is fused is missing. I can add the bond back in using ADT, save it as a pdbqt file, close it, and then reopen it, and it will be gone again.

Has anybody had this problem before?


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PostPosted: Tue Aug 20, 2013 4:37 pm 
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It happened with me also in case of docked files, i think in PDBQT format there is no connection parameter information unlike PDB files, i dont know how to fix, i just put the bond manualy after docking.


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