[modeller_usage] Error in ALIGN_CODES(i)

[Sumedha Roy <>]

Hello all,

When I try to model my protein-DNA complex, I get the error:
_modeller.ModellerError: read_al_373E> Protein specified in ALIGN_CODES(i) was not found in the alignment file; ALIGN_CODES(       2) =  2AHN

But I see no mistake either in the alignment or the format. I've attached both the ALI file and model-ligand.py. Please help!!!

-- 
Sumedha Roy

Attachment: alignment-ligand.ali
Description: Binary data

# Homology modeling with ligand transfer from the template
from modeller import *              # Load standard Modeller classes
from modeller.automodel import *    # Load the automodel class

log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']

# Read in HETATM records from template PDBs
env.io.hetatm = True

a = automodel(env,
              alnfile  = 'alignment-ligand.ali',  # alignment filename
              knowns   = '2AAA',              # codes of the templates
              sequence = '2AHN')              # code of the target
              
a.starting_model= 1                # index of the first model
a.ending_model  = 1                # index of the last model
                                    # (determines how many models to calculate)
a.make()                            # do the actual homology modeling