message: More conservative fix.
  Only impose size limit when box is constructed during minimization.
  For whole protein docking the autobox_ligand might be large
  (autobox_ligand is receptor) and I don't want to artificially limit that, but a 100A ligand by itself is ridiculous.
diff: @@ -1697,15 +1697,6 @@ Thank you!\n";
  if (settings.local_only)
  {
  gdbox = m->movable_atoms_box(autobox_add, box_granularity);
  - } else if(autobox_extend) {
  - //make sure every dimension is large enough for the ligand to fit
  - fl maxdim = m->max_span(0);
  - setup_grid_dims(center_x, center_y, center_z,
  - size_x > maxdim ? size_x : maxdim,
  - size_y > maxdim ? size_y : maxdim,
  - size_z > maxdim ? size_z : maxdim, gdbox);
  - }
  -
  bool skip = false;
  for(unsigned pos = 0; pos < 3; pos++) {
  if(gdbox.elems[pos].n*box_granularity > 100) {
  @@ -1717,6 +1708,14 @@ Thank you!\n";
  }
  if(skip)
  continue;
  + } else if(autobox_extend) {
  + //make sure every dimension is large enough for the ligand to fit
  + fl maxdim = m->max_span(0);
  + setup_grid_dims(center_x, center_y, center_z,
  + size_x > maxdim ? size_x : maxdim,
  + size_y > maxdim ? size_y : maxdim,
  + size_z > maxdim ? size_z : maxdim, gdbox);
  + }
  done(settings.verbosity, log);
  std::vector<result_info>* results =
  