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). And if I don't turn HETATM_IO = 'on' and simply using the code

INCLUDE

SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'seq.ali' SET KNOWNS = '1U19' SET SEQUENCE = '1U20' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1

CALL ROUTINE = 'model'

It works very well and give me the right target file.I am really confused about that.Can anyone give me some suggestion about my code.And I also wanna to ask if i want to take the non-residue atoms into consideration during modeller,is my method right?Thank you for your suggestion.