akiheikk@mappi.helsinki.fi wrote: > I'm a new modeller user trying to model some closely related proteins for > docking purposes. I would like to model the binding site of the ligand as > well as possible. The template file I'm using has the ligand in the binding > site. I would like to know is there an easy way of setting the restraints > for the most important residues?

Modeller will automatically build restraints for you between the ligand and all template Calpha atoms within 10 angstroms. This will often be sufficient. If you want additional restraints, then you should redefine the special_restraints subroutine to add them. See http://salilab.org/modeller/FAQ.html#10

> Also the command SET HETATM_IO allways gives me an error: > > Number of residues in the alignment and pdb files are different: 280 > 282

If you turn on HETATM_IO, then you need to add those HETATM residues to your alignment too. Usually you'd use BLK residues for ligands. See http://salilab.org/modeller/FAQ.html#16

> I would love to see a more thorough tutorial on modelling using restraints.

I'm not sure what you mean - all modeling uses restraints. The advanced tutorial gives an example of adding specific user-defined restraints, at http://salilab.org/modeller/tutorial/advanced.html

Ben Webb, Modeller Caretaker