Awhile back I wanted to get MODELLER 9v1 to place template water molecules into the modeled target sequences. I added
"env.io.water = True" to my python script; then in the ali file
_temp ERTF/wwwwwww _target ERTY/wwwwwww
and incremented the indicated length in fields 3-6 of the structureX line to account for the waters. And all went well.
Attempting to generalize to apply to a single ligand, I added "env.io.hetatm = True" to my python script and in the ali file
_temp ERTF/. _target ERTY/.
The HETATM entries for the ligand ARE in the template PDB file.
Modeller refuses to run with this and in the log file it writes that the alignment and the PDB file have different lengths EVEN THOUGH I have incremented the actual length listed in the ALI file StructureX line in fields 3-6.
In this particular case, the ligand in the template is covalently attached to a residue but I will want to model non-covalently bound ligands as well.