Prabhakar. G. wrote: > I am tring to mutate a particular residue in a protein using the below > script but getting the error, > could someone help, > Error > Traceback (most recent call last): > File "(stdin)", line 93, in ? > File "C:\Program Files\Modeller8v2\modlib\modeller\model.py", line > 220, in generate_topology > io=io.modpt, libs=libs.modpt, **vars) > File "C:\Program Files\Modeller8v2\modlib\modeller\util\top.py", line > 197, in generate_topology > return _modeller.generate_topology(mdl, aln, io, libs, *args) > _modeller.error: gener___479E> Must not use patching residues here. > Residue type index, residue type: 35 > > ------------------------------------------------------------------------------------------------------------------------------------------------------------------ > > command: mod8v2 - < mutate.py 1qhd 2 GLU A > 1qhd.log
Modeller is confused because the 1qhd PDB file has a HETATM connected to the main chain. Modeller knows about the ACE residue type, but thinks it is the CHARMM ACE type, which is a patching residue, not a residue in its own right, and so it doesn't know what to do with the ACE residue.
The simplest solution would be to either manually remove the ACE residue from your PDB file, or set model_segment so that Modeller ignores residue 0. You can always use model.patch() to apply the ACE patch to the first residue, if you want to preserve the acetylated N terminus.
Ben Webb, Modeller Caretaker