Re: [modeller_usage] How to incorporate NAD and water in my model

[Modeller Caretaker <modeller-care@ucsf.edu>]

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
--
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