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I modelled a macromolecule/receptor using Avogadro and exported it as receptor.pdb. Many entries in this file are CONECT records. If I try to run AutoDock Vina with it, this happens:

enter image description here

So, if I prepare this receptor again for docking, but, this time, removing the CONECT records (as I've seen many people do), my receptor file now exhibits broken bonds. Like this:

enter image description here

I've tried converting the .pdb file to .pdbqt with OpenBabel — removing all but the largest contiguous fragment and ignoring CONECT records as well —, but nothing works. I've also looked into it, and it looks like Vina doesn't have any parameters to handle CONECT records. Isn't there any way at all to do this?

Thank you in advance.

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    $\begingroup$ Hey, @M__! I'm sorry for not doing this sooner. I was a little short on time yesterday. What about now? Is there anything else I should add? $\endgroup$
    – ginn
    yesterday
  • $\begingroup$ Hi, thats its better. If you copy and paste the ascii characters thats preferred to screen shots for the error output. $\endgroup$
    – M__ ♦
    yesterday

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