Including water molecules, HETATM residues, and hydrogen atoms

If your template contains a ligand (or other HETATM residue) then MODELLER can transfer this into your generated model. This is done first by setting env.io.hetatm to True, which instructs MODELLER to read HETATM records from your template PDB files, and then by using the BLK ('.') residue type in your alignment (both in the template(s) and the model sequence) to copy the ligand(s) as a rigid body into the model.

Example: examples/automodel/model-ligand.py

# Homology modeling with ligand transfer from the template
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = './:../atom_files'

# Read in HETATM records from template PDBs
env.io.hetatm = True

a = automodel(env,
              alnfile  = 'align-ligand.ali',  # alignment filename
              knowns   = '5fd1',              # codes of the templates
              sequence = '1fdx')              # code of the target
a.starting_model= 4                 # index of the first model 
a.ending_model  = 4                 # index of the last model
                                    # (determines how many models to calculate)
a.make()                            # do the actual homology modeling

Note that by turning on env.io.hetatm, all HETATM records are read, so all of these must be listed in your alignment.

You can also treat ligands flexibly by defining topology and parameter information. See section 5.2.1 for more information, and the example in the advanced modeling tutorial, at http://salilab.org/modeller/tutorial/advanced.html.

If you want to add ligands to your model which are not present in your template, you will need to do some docking studies, which are beyond the scope of the MODELLER program.

To read in water residues, set env.io.water to True and use the 'w' residue type in your alignment.

To read in hydrogen atoms, set env.io.hydrogen to True. This is not generally necessary, as if you want to build an all hydrogen model, it is easiest just to use the allhmodel class, which turns this on for you automatically; see section 2.2.4.