[modeller_usage] Question about restraints

Hi, 

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? Should I use the MAKE_RESTRAINTS command
somehow or is it more reliable to use another program like Sybyl or Insight
to choose the restraints? Also the command SET HETATM_IO allways gives me an
error:

Number of residues in the alignment and  pdb files are different:      280 
    282
Might this be related to the fact that there are two phosphorylated residues
 in the template? 

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


[Aki]

Aki Heikkilä 
Department of pharmaceutical chemistry 
University of Helsinki