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: : MCLPTIRKIAIIGAGPSGLVTAKALLAEKAFDQVTLFERRGSPGGVWNYTSTLSNKLPVP STNPILTTEPIVGPAALPVYPSPLYRDLQTNTPIELMGYCDQSFKPQTLQFPHRHTIQEY QRIYAQ--PLLPFIKLATDVLDIE-----KKDGSWVVTYKGTKAGSPISKDIFDAVSICNGHYEVPYIPNI-- KGLDEYAKAVPGSVLHSSLFREPELFVGESVLVVGGASSANDLVRHLTPVAKHPIYQSLL GG--------------------------------------------------------- GDIQNES--------------LQQVPEITKFDPTTREIYLKGGKVLSNIDR VIYCTGYLYSVPFPSLAKLKSPETKLIDDGSHVHNVYQHIFYIPDPTLAFVGLALH- VVPFPTSQAQAAFLARVWSGRLKLPSKEEQLKWQDELMFSLSGANNMYHSLDYPKD---ATYINKLH--------- DWCKQATPVLEEE-FP------------SPYWGEKERSIRENMWSIRAK----- FFGI-EPPK-----------------------..* >P1;P31513 sequence:P31513:0:.:0:.:flavin-containing monooxidase 3:homo sapiens: : ----MGKKVAIIGAGVSGLASIRSCLEEGL--EPTCFEKSNDIGGLWKFSDHAEEGR----- -------------------ASIYKSVFSNSSKEMMCFPDFPFPDDFPNF MHNSKIQEYIIAFAKEKNLLKYIQFKTFVSSVNKHPDFATTGQWDVTTER--- DGKKESAVFDAVMVCSGHHVYPNLPKESFPGLN----HFKGKCFHSRDYKEPGVFNGKRVLVVGLGN SGCDIATELSRTAEQVMISSRSGSWVMSRVWDNGYPWDMLLVTRFGTFLKNNLPTAISDW LYVKQMNARFKHENYGLMPLNGVLRKEPVFNDELPASILCGIVSVKPNVKEF-- TETSAIFEDGTIFEGIDCVIFATGYSFAYPFLDESIIKSRNNEIILFKG----VFPPL-- LEKSTIAVIGFVQSLGAAIPTVDLQSRWAAQVIKGTCTLPSMEDMMNDINEKMEKK---RKWFG- KSETIQTDYIVYMDELSSFIGAKPNIPWLFLTDPKLAMEVYFGPCSPYQFRLVGPGQWPGARNAI- LTQWDRSLKPMQTRVVGRLQKPCFFFHWLKLFAIPILLIAVFLVLT..*
Please point out my mistakes. Your help is so much appreciated. Thanks in advance
Fadhila Balqis Nurfitria