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



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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