Re: [modeller_usage] Modeling Ligand from non-homologous protein

[Modeller Caretaker <>]

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
--
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