Dear Modeller Users!

I've forced with the problem during preparation of the model of my Green Fluorescent protein.

In particular this model consist of heteroatomic chromophore group which is the part of the protein polypeptide chain. Because my initial pdb file have missed N term (first 1-10 residues) I'd like to build full-residue model including chromophore group which present in the pdb file as the HETATM.

below you can see my alignment file as well as script

>P1;input
structureX:input:6:    ::225 : ::-1.00:-1.00
-----NVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQ.SKVYVKHPADIP
DYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGE
IHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL*

>P1;seq
sequence:seq:     : :     : ::: 0.00: 0.00
MRSSKNVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQ.SKVYVKHPADIP
DYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGE
IHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHLFL*

# Homology modeling with multiple templates
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
# Read in HETATM records from template PDBs
env.io.hetatm = True
# directories for input atom files
env.io.atom_files_directory = ['.', '../atom_files']
allow_alternates=True

a = automodel(env,
              alnfile = 'align-multiple_new.ali', # alignment filename
              knowns   = 'input',     # codes of the templates
              sequence = 'seq')               # code of the target

a.starting_model= 1                 # index of the first model
a.ending_model = 30                # index of the last model
                                    # (determines how many models to calculate)
a.make()                            # do the actual homology modeling

Here in both sequences dot (.) in the SPQ.SK motif correspond to the chromophore group (env.io.hetatm = True). Unfortunatelly I have error after processing this

_modeller.SequenceMismatchError: get_ran_648E> Alignment sequence not found in PDB file:        1 ./input.pdb (You didn't specify the starting and ending residue numbers and chain IDs in the alignment, so Modeller tried to guess these from the PDB file.) Suggestion: put in the residue numbers and chain IDs (see the manual) and run again for more detailed diagnostics. You could also try running with allow_alternates=True to accept alternate one-letter code matches (e.g. B to N, Z to Q).

How I could fix it ?

Thanks for help,

James