[modeller_usage] ALIGN CODES NOT FOUND

[Fadhila Balqis N <>]

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