Dear All,

I want to make a model by using this specific template "2GVC" and I try to include HETATM residues to my model. But then this happened:

openf___224_> Open           $(LIB)/restyp.lib
openf___224_> Open           ${MODINSTALL9v17}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups:        2
openf___224_> Open           ${MODINSTALL9v17}/modlib/sstruc.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       191566     187.076     0.183

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       192094     187.592     0.183
openf___224_> Open           ${MODINSTALL9v17}/modlib/resdih.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       240694     235.053     0.230
rdrdih__263_> Number of dihedral angle types         :        9
              Maximal number of dihedral angle optima:        3
              Dihedral angle names                   :  Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5
openf___224_> Open           ${MODINSTALL9v17}/modlib/radii.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:       253994     248.041     0.242
openf___224_> Open           ${MODINSTALL9v17}/modlib/radii14.lib
openf___224_> Open           ${MODINSTALL9v17}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes:  APBLE
openf___224_> Open           ${MODINSTALL9v17}/modlib/mnch.lib
rdclass_257_> Number of classes:        5
openf___224_> Open           ${MODINSTALL9v17}/modlib/mnch1.lib
openf___224_> Open           ${MODINSTALL9v17}/modlib/mnch2.lib
openf___224_> Open           ${MODINSTALL9v17}/modlib/mnch3.lib
openf___224_> Open           ${MODINSTALL9v17}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types:       21
openf___224_> Open           align-ligand.ali

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       265487     259.265     0.253

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       266937     260.681     0.255

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       269837     263.513     0.257

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       275637     269.177     0.263

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       287237     280.505     0.274

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       310437     303.161     0.296

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:       325013     317.396     0.310
read_al_373E> Protein specified in ALIGN_CODES(i) was not found
              in the alignment file; ALIGN_CODES(       2) =  P31513

I used this script:

# Comparative 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  = 'align-ligand.ali',  # alignment filename
              knowns   = '2gvc',              # codes of the templates
              sequence = 'P31513')            # code of the target
a.starting_model= 4                 # index of the first model
a.ending_model  = 4                 # index of the last model
                                    # (determines how many models to calculate)
a.make()                            # do the actual comparative modeling

and used this alignment format:

>P1;2gvc
structureX:2gvc:5: :575: :flavin-containing monooxidase:saccharomyces pombe: : 
MCLPTIRKIAIIGAGPSGLVTAKALLAEKAFDQVTLFERRGSPGGVWNYTSTLSNKLPVPSTNPILTTEPIVGPAALPVYPSPLYRDLQTNTPIELMGYCDQSFKPQTLQFPHRHTIQEYQRIYAQ--PLLPFIKLATDVLDIE-----KKDGSWVVTYKGTKAGSPISKDIFDAVSICNGHYEVPYIPNI--KGLDEYAKAVPGSVLHSSLFREPELFVGESVLVVGGASSANDLVRHLTPVAKHPIYQSLLGG---------------------------------------------------------GDIQNES--------------LQQVPEITKFDPTTREIYLKGGKVLSNIDRVIYCTGYLYSVPFPSLAKLKSPETKLIDDGSHVHNVYQHIFYIPDPTLAFVGLALH-VVPFPTSQAQAAFLARVWSGRLKLPSKEEQLKWQDELMFSLSGANNMYHSLDYPKD---ATYINKLH---------DWCKQATPVLEEE-FP------------SPYWGEKERSIRENMWSIRAK-----FFGI-EPPK-----------------------..*
>P1;P31513
sequence:P31513:0:.:0:.:flavin-containing monooxidase 3:homo sapiens: : 
----MGKKVAIIGAGVSGLASIRSCLEEGL--EPTCFEKSNDIGGLWKFSDHAEEGR------------------------ASIYKSVFSNSSKEMMCFPDFPFPDDFPNFMHNSKIQEYIIAFAKEKNLLKYIQFKTFVSSVNKHPDFATTGQWDVTTER---DGKKESAVFDAVMVCSGHHVYPNLPKESFPGLN----HFKGKCFHSRDYKEPGVFNGKRVLVVGLGNSGCDIATELSRTAEQVMISSRSGSWVMSRVWDNGYPWDMLLVTRFGTFLKNNLPTAISDWLYVKQMNARFKHENYGLMPLNGVLRKEPVFNDELPASILCGIVSVKPNVKEF--TETSAIFEDGTIFEGIDCVIFATGYSFAYPFLDESIIKSRNNEIILFKG----VFPPL--LEKSTIAVIGFVQSLGAAIPTVDLQSRWAAQVIKGTCTLPSMEDMMNDINEKMEKK---RKWFG-
KSETIQTDYIVYMDELSSFIGAKPNIPWLFLTDPKLAMEVYFGPCSPYQFRLVGPGQWPGARNAI-LTQWDRSLKPMQTRVVGRLQKPCFFFHWLKLFAIPILLIAVFLVLT..*

Please point out my mistakes. Your help is so much appreciated.
Thanks in advance



Fadhila Balqis Nurfitria