Could you share the first few lines of your
mol2 file? They should look like that (from the aspirin example):
20 20 0 0 0
If I understand the error message correctly, one of the molecules in your file looks like that:
so the third field (substructure) is missing. If that is indeed the case, I suspect you have not installed the latest version of
bio3d, which automatically fills in the missing fields. The one on CRAN should do it, try running
You could try with the option
maxlines if this worries you. Check your file first to avoid cutting in the middle of a molecule.