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:
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:
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.