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Most likely your PDB file is a PalmDOC PDB. In that case it's just a TXT file inside of the PDB container. TXT tries to auto detect the formatting. Sometimes it gets it wrong and the formatting comes out wrong in a conversion. Unfortunately, PDB input does not allow you to specify the formatting (TXT does). I can be sure this is happening if you post the conversion log. If this is the case you can try a tool like pdbshread and extract the TXT from the PDB then you will have more options and control over the conversion.
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