Unable to get molecule whole/bonds broken

I am on GROMACS 5.1 and have used SwissParam to generate topology for cyclodextrin.
After doing the usual steps to get grompp working fine, i changed output file from .gro to .pdb using editconf and i got this visual.

I have tried using gmx trjconv to get the PBC removed but im unsure which option to pick, or if its even due to PBC that molecule bonds are broken. Atoms are also out of the solvent box as well.

What does this mean? Renaming atoms? If you haven’t been careful to preserve column alignment in your .pdb file, you will get mangled coordinates.

it might have been this step after copying atom names from itp to pdb.

i wasnt sure how to align this but somehow after aligning to the best i can, grompp didnt show fatal error


Thanks Justin! Realised it was an alignment error and I saw the column number wrongly. Have solved this issue. Thanks a lot for the link too J great to always have on hand