When the client connects, sometimes DNS resolution of the host is internal.
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Your PDB contains gold atoms, and Open Babel doesn't know how to handle the "AU" atoms. That's what's causing Open Babel to choke. Parsing this is tricky, though, as it doesn't always work. Older PDBs (and lazy PDB-outputting software) don't do that.įor the most part that works, as the atom name entry normally contains the element designation. Basically, the official PDB specification requires that the atom names be present off to the right-hand side of each ATOM/HETATM line. This thread from the OpenBabel mailing list goes into more details. Problems reading a HETATM or ATOM record.Ĭolumns 77-78 should contain the element symbol of an atom. *** Open Babel Warning in parseAtomRecord If you take a look at the output, you see a bunch of the following warnings. The conversion issue you're seeing is because the PDB you're using is not technically well-formatted.
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