hi,
I am facing a great problem with modeller 9v3.
My aim is to model 2 chain protein from a 2 chain template with a ligands. I want two ligands: so4 and PLP . Last part of my template pdb file briefly looks like this:
ATOM 6617 CG LYS B 438 1.294 41.930 2.754 1.00 92.99 C
ATOM 6618 CD LYS B 438 -0.149 41.634 3.105 1.00 93.43 C
ATOM 6619 CE LYS B 438 -0.497 40.199 2.765 1.00 93.98 C
ATOM 6620 NZ LYS B 438 -1.930 39.900 3.035 1.00 94.74 N
ATOM 6621 OXT LYS B 438 4.571 44.878 1.525 1.00 92.93 O
TER 6622 LYS B 438
HETATM 6623 S SO4 600 2.001 43.793 71.949 0.40 47.42 S
HETATM 6624 O1 SO4 600 1.250 44.661 72.856 1.00 49.68 O
HETATM 6625 O2 SO4 600 3.441 43.960 72.132 1.00 48.63 O
HETATM 6626 O3 SO4 600 1.702 42.399 72.263 1.00 51.95 O
HETATM 6627 O4 SO4 600 1.623 44.087 70.571 1.00 47.72 O
HETATM 6628 S SO4 601 -1.057 44.770 34.953 0.40 54.22 S
HETATM 6629 O1 SO4 601 -0.255 45.682 34.134 1.00 54.47 O
HETATM 6630 O2 SO4 601 -2.472 45.080 34.803 1.00 53.56 O
HETATM 6631 O3 SO4 601 -0.879 43.378 34.512 1.00 56.11 O
HETATM 6632 O4 SO4 601 -0.655 44.930 36.347 1.00 55.09 O
HETATM 6633 N1 PLP A 500 6.942 41.456 67.024 1.00 91.96 N
HETATM 6634 C2 PLP A 500 7.237 41.844 68.301 1.00 92.40 C
HETATM 6635 C2A PLP A 500 8.277 41.064 69.104 1.00 91.84 C
HETATM 6636 C3 PLP A 500 6.579 42.967 68.880 1.00 91.52 C
HETATM 6637 O3 PLP A 500 6.876 43.351 70.176 1.00 90.45 O
HETATM 6638 C4 PLP A 500 5.613 43.677 68.118 1.00 90.22 C
HETATM 6639 C4A PLP A 500 4.901 44.884 68.713 1.00 86.77 C
HETATM 6640 C5 PLP A 500 5.327 43.248 66.794 1.00 91.55 C
HETATM 6641 C6 PLP A 500 6.014 42.124 66.269 1.00 92.40 C
HETATM 6642 C5A PLP A 500 4.287 43.977 65.936 1.00 92.05 C
HETATM 6643 O4P PLP A 500 4.919 44.983 65.137 1.00 91.48 O
HETATM 6644 P PLP A 500 3.850 45.746 64.212 0.40 89.98 P
HETATM 6645 O1P PLP A 500 2.942 46.559 65.059 1.00 90.28 O
HETATM 6646 O2P PLP A 500 3.052 44.763 63.428 1.00 89.69 O
HETATM 6647 O3P PLP A 500 4.581 46.636 63.284 1.00 90.10 O
HETATM 6648 N1 PLP B 501 -5.783 42.808 39.108 1.00 86.12 N
HETATM 6649 C2 PLP B 501 -5.828 43.152 37.781 1.00 84.21 C
HETATM 6650 C2A PLP B 501 -6.726 42.368 36.828 1.00 82.77 C
HETATM 6651 C3 PLP B 501 -5.053 44.236 37.298 1.00 83.34 C
HETATM 6652 O3 PLP B 501 -5.098 44.562 35.960 1.00 81.37 O
HETATM 6653 C4 PLP B 501 -4.219 44.961 38.203 1.00 83.20 C
HETATM 6654 C4A PLP B 501 -3.382 46.155 37.713 1.00 78.97 C
HETATM 6655 C5 PLP B 501 -4.188 44.570 39.573 1.00 85.23 C
HETATM 6656 C6 PLP B 501 -4.989 43.485 40.001 1.00 85.99 C
HETATM 6657 C5A PLP B 501 -3.301 45.301 40.567 1.00 87.11 C
HETATM 6658 O4P PLP B 501 -4.052 45.705 41.701 1.00 89.48 O
HETATM 6659 P PLP B 501 -3.055 46.187 42.850 0.40 90.61 P
HETATM 6660 O1P PLP B 501 -2.152 47.241 42.323 1.00 89.77 O
HETATM 6661 O2P PLP B 501 -2.247 45.036 43.343 1.00 89.52 O
HETATM 6662 O3P PLP B 501 -3.851 46.742 43.973 1.00 90.54 O
HETATM 6663 O HOH 1 -2.199 65.598 27.605 1.00 37.63 O
HETATM 6664 O HOH 2 13.146 43.997 69.980 1.00 28.90 O
HETATM 6665 O HOH 3 3.514 34.147 84.461 1.00 40.65 O
HETATM 6666 O HOH 4 14.245 36.668 40.667 1.00 33.18 O
HETATM 6667 O HOH 5 6.748 58.168 71.500 1.00 37.09 O
HETATM 6668 O HOH 6 -3.541 20.765 51.638 1.00 34.79 O
HETATM 6669 O HOH 7 -4.102 61.235 21.691 1.00 38.94 O
HETATM 6670 O HOH 8 10.326 70.845 65.572 1.00 35.43 O
HETATM 6671 O HOH 9 -4.995 51.193 45.379 1.00 38.86 O
HETATM 6672 O HOH 10 -6.557 33.928 65.811 1.00 39.72 O
HETATM 6673 O HOH 11 -1.108 49.863 77.220 1.00 41.22 O
HETATM 6674 O HOH 12 -26.403 30.845 53.499 1.00 43.93 O
HETATM 6675 O HOH 13 -6.662 49.811 60.632 1.00 20.93 O
HETATM 6676 O HOH 14 0.524 46.344 51.157 1.00 30.77 O
HETATM 6677 O HOH 15 4.444 27.533 53.723 1.00 45.47 O
HETATM 6678 O HOH 16 -9.377 50.142 40.921 1.00 38.67 O
HETATM 6679 O HOH 17 16.732 42.270 53.224 1.00 43.17 O
HETATM 6680 O HOH 18 36.203 41.041 67.666 1.00 41.06 O
HETATM 6681 O HOH 19 -23.753 42.588 51.308 1.00 39.07 O
my alignment looks like this
>P1;1iax
structureX:1iax:11 :A :438 :B :ferredoxin:Azotobacter vinelandii: 1.90: 0.19
ILSKLATNE-----SPYFDGWKAYDSDPFHPLKNPNGVIQMGLAENQLCLDLIEDWIKRN
PKGSIS-------FKAIANFQDYHGLPEFRKAIAKFMEKTRGGRVRFDPERVVMAGGATG
ANETIIFCLADPGDAFLVPSPYYPAFNRDLRWRTGVQLIPIHCESSNNFKITSKAVKEAY
ENAQKSNIKVKGLILTNPSNPLGTTLDKDTLKSVLSFTNQHNIHLVCDEIYAATVFDTPQ
FVSIAEILDEQEMTYCNKDLVHIVYSLSKDMGLPGFRVGIIYSFNDDVVNCARKMSSFGL
VSTQTQYFLAAMLSDEKFVDNFLRESAMRLGKRHKHFTNGLEVVGIKCLKNNAGLFCWMD
LRPLLRESTFDSEMSLWRVIINDVKLNVSPGSSFECQEPGWFRVCFANMDDGTVDIALAR
IRRFVGVEK/ILSKLATNE-----SPYFDGWKAYDSDPFHPLKNPNGVIQMGLAENQLCLD
LIEDWIKRNPKGSIS-------FKAIANFQDYHGLPEFRKAIAKFMEKTRGGRVRFDPER
VVMAGGATGANETIIFCLADPGDAFLVPSPYYPAFNRDLRWRTGVQLIPIHCESSNNFKI
TSKAVKEAYENAQKSNIKVKGLILTNPSNPLGTTLDKDTLKSVLSFTNQHNIHLVCDEIY
AATVFDTPQFVSIAEILDEQEMTYCNKDLVHIVYSLSKDMGLPGFRVGIIYSFNDDVVNC
ARKMSSFGLVSTQTQYFLAAMLSDEKFVDNFLRESAMRLGKRHKHFTNGLEVVGIKCLKN
NAGLFCWMDLRPLLRESTFDSEMSLWRVIINDVKLNVSPGSSFECQEPGWFRVCFANMDD
GTVDIALARIRRFVGVEK/..*
>P1;1fdx
sequence:1fdx: : : : :ferredoxin:Peptococcus aerogenes: 2.00:-1.00
ILSRIATNDGHGENSSYFDGWKAYEKDPFHLTDNPTGVIQMGLAENQLSLDLIRDWMKKN
PQASICTEEGVSEFKAIANFQDYHGLPTFRKAIAQFMEKVRGGRTRFDPDRIVMSGGATG
AQETIAFCLADPGEAFLIPTPYYPGFDR-FRWRTGVQLLPIHCHSSNKFKITQAALETAY
RKARNSHIRVKGILVTNPSNPLGTTMDRETLRTLVSFVNEKRMHLVCDEIFSGTAFDKPS
YVSVSEVIEDE--PYCDRDLIHIAYSLSKDLGVPGFRVGVIYSYNDAVVSCARKMSSFGL
VSSQTQHLLASMLGDEELTTSFLATSRTGLCGRRRVFTDGLKRVGIHCLDGNAGLFCWMD
LRPLLKEATVEAELRLWRVIINDVKLNISPGSSFHCSEPGWFRVCFANMDDTAMKIALRR
IESFVYREN/ILSRIATNDGHGENSSYFDGWKAYEKDPFHLTDNPTGVIQMGLAENQLSLD
LIRDWMKKNPQASICTEEGVSEFKAIANFQDYHGLPTFRKAIAQFMEKVRGGRTRFDPDR
IVMSGGATGAQETIAFCLADPGEAFLIPTPYYPGFDR-FRWRTGVQLLPIHCHSSNKFKI
TQAALETAYRKARNSHIRVKGILVTNPSNPLGTTMDRETLRTLVSFVNEKRMHLVCDEIF
SGTAFDKPSYVSVSEVIEDE--PYCDRDLIHIAYSLSKDLGVPGFRVGVIYSYNDAVVSC
ARKMSSFGLVSSQTQHLLASMLGDEELTTSFLATSRTGLCGRRRVFTDGLKRVGIHCLDG
NAGLFCWMDLRPLLKEATVEAELRLWRVIINDVKLNISPGSSFHCSEPGWFRVCFANMDD
TAMKIALRRIESFVYREN/..*
and mt python script is
# 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 = 'align-ligand.ali', # alignment filename
knowns = '1iax', # codes of the templates
sequence = '1fdx') # 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 homology modeling
but it ends with following error
# Code #_Res #_Segm PDB_code Name
-------------------------------------------------------------------------------
1 1iax 836 3 1iax ferredoxin
2 1fdx 854 3 1fdx ferredoxin
check_a_343_> >> BEGINNING OF COMMAND
openf___224_> Open ./\1iax.pdb
Dynamically allocated memory at amaxstructure [B,KiB,MiB]: 4277067 4176.823 4.079
openf___224_> Open ./\1iax.pdb
read_te_290E> Number of residues in the alignment and pdb files are different: 836 834
For alignment entry: 1 1iax
x (mismatch at alignment position 835)
Alignment VDIALARIRRFVGVEK..
PDB VDIALARIRRFVGVEK
Match ****************
Please check your alignment file header to be sure you correctly specified
the starting and ending residue numbers and chains. The alignment sequence
must match that from the atom file exactly.
Another possibility is that some residues in the atom file are missing,
perhaps because they could not be resolved experimentally. (Note that Modeller
reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.)
In this case, simply replace the section of your alignment corresponding
to these missing residues with gaps.
read_te_288W> Protein not accepted: 1 1iax
Please solve this puzzle as i am fade-up with this :(
regards
sanjay