[modeller_usage] Question on an error message

["Cen Gao" <>]

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.