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PostPosted: Mon Jun 23, 2014 8:03 pm 
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Joined: Mon Jun 23, 2014 7:57 pm
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When I change my ligand from a .pdb file to a .pdbqt file, the ligand seems to automatically have some bonds that are important removed. it modifies the bonds around the ring structure of the ferrocene. I have looked at everything and cannot figure out why this happend or how to prevent it from happening, as to use vina I need the file as a .pdbqt. I have attached the files so you can see what I mean.
Attachment:
1_SR_11.pdbqt [5.24 KiB]
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Attachment:
1-SR-11.pdb [7.71 KiB]
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