Reply To: how to keep native structure when do loop modeling

[Anonymous]

It’s probably balking because something is wrong with the sidechains at those positions – most likely either the hydrogens are labeled improperly (and ignored) or there are heavy atoms missing, or both. Rosetta won’t tolerate missing atoms and will build them back in; it then repacks the sidechain to ensure the newly built atoms don’t clash.

These changes are probably occuring at the time of PDB read-in, not within loop modeling (thus loops: natsc didn’t work).

Try -pack::pack_missing_sidechains false. It defaults true so you need the false.

If the moving sidechains are far from your loop you they won’t affect its conformation – you can also just fix them by editing the PDB later.