Cen Gao wrote: > Hi, I am new to modeller,Now I am just doing some simple test on a protein,but both the target and template has some atom file other than residue which i have to consider during the simulation.So i have to include the HETATM_IO = 'on' in simulation,my top file is as follow: > > INCLUDE > > SET OUTPUT_CONTROL = 1 1 1 1 1 > SET ALNFILE = 'seq.ali' > SET KNOWNS = '1U19' > SET SEQUENCE = '1U20' > SET TOPOLOGY_MODEL = 1, HETATM_IO = 'on', WATER_IO = 'on' > SET TOPLIB = '$(LIB)/top.lib' > SET PARLIB = '$(LIB)/par.lib' > SET STARTING_MODEL = 1 > SET ENDING_MODEL = 1 > > CALL ROUTINE = 'model' > > But it give me some error information > > rdabrk__290E> Number of residues in the alignment and pdb files are different: 696 697 > For alignment entry: 1 > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > I don't why,because the alignment file and pdb file is exactly right(I simply generate the alignment file from the pdb file using modeller).
It's hard to tell, since you didn't post your alignment file, but you need to include the ligand (e.g. with a BLK residue). See http://salilab.org/modeller/tutorial/advanced.html for an example.
Ben Webb, Modeller Caretaker