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