Respected Sir 

                   i am trying to add my model one zinc HETATM, but my efforts are failed , iam getting ATOM in my file pdb instead HETATM 
in the template structure Experimentally solved Residues Region 191-609 , protein Total Length: 419 in that Five residue are Missing Residue 

Here i mentioned  

Alignment file 

>P1;2DW0
structureX:2DW0.pdb: 196 :A:+414 :A:MOL_ID  1; MOLECULE  CATROCOLLASTATIN; CHAIN  A, B; FRAGMENT  RESIDUES 191-609; SYNONYM  VAP2, VASCULAR APOPTOSIS-INDUCING PROTEIN-2, CATROCOLLASTATIN/VAP2B:MOL_ID  1; ORGANISM_SCIENTIFIC  CROTALUS ATROX; ORGANISM_COMMON  WESTERN DIAMONDBACK RATTLESNAKE; ORGANISM_TAXID  8730: 2.15: 0.17
PFRFVELVLVVDKAMVTKNNGDLDKIKTRMYEIVNTVNEIYRYMYIHVALVGLEIWSNEDKITVKPEAGYTLNAF
GEWRKTDLLTRKKHDNAQLLTAIDLD-RVIGLAYVGSMCHPKRSTGIIQDYSEINLVVAVIMAHEMGHNLGINHD
SGYCSCGDYACIMRPEISPEPSTFFSNCSYFECWDFIMNHNPECILNEPLGTDIISPPVCGNELLEVGEECDCGT
PENCQNECCDAATCKLKSGSQCGHGDCCEQCKFSKSGTECRASMSECDPAEHCTGQSSECPADVFHKNGQPCLDN
YGYCYNGNCPIMYHQCYDLFGADVYEAEDSCFERNQKGNYYGYCRKENGNKIPCAPEDVKCGRLYCKDNSPGQNN
PCKMFYSNEDEHKGMVLPGTKCADGKVCSNGHCVDVATAY.*

>P1;TvLDH
sequence:TvLDH:     : :     : ::: 0.00: 0.00
P-RYIELVIVADRAMVTKNNGDLTAIRTWVHQIVNDMTVMYRDLNIHITLAAVVIWNKRDLITVTSSAEDTLNLF
GTWRETKYLKHRKHDNAQLLTGIILDDDTIGLAYVGGMCDPKKSVGIIEDHSTEHLLVAATMAHEMGHNLGMNHD
ANQCNCGANGCVMSATLTEQTSYQFSDCSKDEYQNYLTDHNPQCILNQPLRTD-T-P-VSRNELLQ-NSAHPC--
--------CDPVTCQPK--RFCVSGPCCENCQFVRAGTVCNPAKGD-WMDDYCTGISSDCPRNPL----------
-----NGFR------------------------------------------------------------------
----------------------------------------.*

and 

Model Ligand python script which i used as followed 


# 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  = 'TvLDH-2DW0A.ali',  # alignment filename
              knowns   = '2DW0',              # codes of the templates
              sequence = 'TvLDH')              # code of the target
a.starting_model= 1                 # index of the first model
a.ending_model  = 5                 # index of the last model
                                    # (determines how many models to calculate)
a.make()                            # do the actual homology modeling


kindly give provide your valuable suggestion regarding error 





--
Regards,
S.VENKATESH,