deepti wrote: > I am trying to construct a model for a protein having a known > structure for the purpose of learning Modeller. > The pdb structureis in form of protein-NAD adduct. My aim is to build a > similar model. > Using the templates I have built a model, please tell me how to > incorporate NAD and water in my model. I have read the manual 'faq' , > but am confused how to change my alignment (including '.' for BLK > residues and 'w' ). How do I change the template pdb files for this? > How do I make my own restraint file?
There is no need to change your PDB file, or define custom restraints. You simply tell Modeller to read in the HETATM and water residues from the PDB (env.io.hetatm = True and env.io.water = True) and then list all of those residues in your template sequence in your alignment (. for HETATM, w for water). You can then use the target sequence alignment as per usual to list the residues you want to appear in your final model (generally people use a 1:1 alignment for the . and w residues).
There is a fully functional example in the manual at http://salilab.org/modeller/manual/node18.html (you can find the model-ligand.py and align-ligand.ali inputs in the examples/automodel directory). Alternatively, the advanced modeling tutorial at http://salilab.org/modeller/tutorial/advanced.html goes into some detail on ligand modeling, complete with custom restraints.
If this information is not clear, please let me know.
Ben Webb, Modeller Caretaker