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Re: [modeller_usage] ligand modeling in binding site of protein

mahendra awale wrote:
...
File "/usr/local/modeller8v2/modlib/modeller/util/top.py", line 329, in add_restraint 
return _modeller.add_restraint(mdl, *args)
_modeller.error: add_res_442E> One or more atoms absent from MODEL: N1:101 N3:13
This suggests that you have tried to add some extra restraints by overriding the special_restraints method in automodel - but the atoms you have asked to restrain do not exist. Note that the atom names should be the PDB names (there is no N1 or N3 atom in any of the standard amino acids), and the residue numbers must match the numbering in your model, not in the template. (Also, if you have multiple chains, you may need to also specify a chain ID.) Check the initial unoptimized model (.ini file) to be sure of the atom and residue naming.
I recommend that you actually use Modeller 9v2 rather than 8v2, which has more robust support for user-defined restraints. You can find a suitable example at http://salilab.org/modeller/9v2/manual/node27.html 

	Ben Webb, Modeller Caretaker
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