On 7/15/13 2:59 PM, Rohitesh Gupta wrote: > I am unable to understand the process of moving the ligand in 1emd_bs > beyond the upper bound?
The coordinates of the ligand were modified in the PDB file, using a text editor.
> As in, how does one not let modeller choose the > default restraints from the template
Modeller automatically restrains certain distances to resemble the template, so that ligands end up in the right place. See http://salilab.org/modeller/9.12/manual/node70.html The last entry in the list on that page is the important one here - ligands are restrained to stay near protein CA atoms. By moving the ligand away, those restraints won't be added. Instead, the manually added ligand-CA restraints will be (and these will pull the ligand back into the correct position during modeling).
Ben Webb, Modeller Caretaker