<P>
My aim is to model single chain protein from a 2 chain template with 2 ligands ( PLP).following the advance tutorial I have edited template PDB ( i.e.1IAX) as per my requirement.I have deleted chain B in the ligand which will interact with it.now template is look like this-<BR>
<BR>
ATOM 2020 N SER A 277 6.836 50.703 64.530 1.00 50.02 N <BR>
ATOM 2021 CA SER A 277 5.736 50.683 65.488 1.00 52.57 C <BR>
ATOM 2022 C SER A 277 6.158 50.953 66.920 1.00 53.76 C <BR>
ATOM 2023 O SER A 277 5.656 51.877 67.558 1.00 53.78 O <BR>
ATOM 2024 CB SER A 277 5.023 49.340 65.432 1.00 53.52 C <BR>
ATOM 2025 OG SER A 277 4.399 49.181 64.168 1.00 60.54 O <BR>
ATOM 2026 N LYS A 278 7.083 50.145 67.425 1.00 55.18 N <BR>
ATOM 2027 CA LYS A 278 7.540 50.304 68.795 1.00 56.49 C <BR>
ATOM 2028 C LYS A 278 8.430 51.529 69.009 1.00 56.08 C <BR>
ATOM 2029 O LYS A 278 8.170 52.321 69.915 1.00 56.54 O <BR>
ATOM 2030 CB LYS A 278 8.218 49.013 69.274 1.00 59.46 C <BR>
ATOM 2031 CG LYS A 278 7.268 47.807 69.271 1.00 63.38 C <BR>
ATOM 2032 CD LYS A 278 6.048 48.015 70.191 1.00 69.44 C <BR>
ATOM 2033 CE LYS A 278 4.984 46.952 69.962 1.00 73.69 C <BR>
ATOM 2034 NZ LYS A 278 5.598 45.765 69.377 1.00 82.22 N <BR>
TER 2035 LYS A 278 <BR>
HETATM 6623 S SO4 600 2.001 43.793 71.949 0.40 47.42 S <BR>
HETATM 6624 O1 SO4 600 1.250 44.661 72.856 1.00 49.68 O <BR>
HETATM 6625 O2 SO4 600 3.441 43.960 72.132 1.00 48.63 O <BR>
HETATM 6626 O3 SO4 600 1.702 42.399 72.263 1.00 51.95 O <BR>
HETATM 6627 O4 SO4 600 1.623 44.087 70.571 1.00 47.72 O <BR>
HETATM 6633 N1 PLP A 500 6.942 41.456 67.024 1.00 91.96 N <BR>
HETATM 6634 C2 PLP A 500 7.237 41.844 68.301 1.00 92.40 C <BR>
HETATM 6635 C2A PLP A 500 8.277 41.064 69.104 1.00 91.84 C <BR>
HETATM 6636 C3 PLP A 500 6.579 42.967 68.880 1.00 91.52 C <BR>
HETATM 6637 O3 PLP A 500 6.876 43.351 70.176 1.00 90.45 O <BR>
HETATM 6638 C4 PLP A 500 5.613 43.677 68.118 1.00 90.22 C <BR>
HETATM 6639 C4A PLP A 500 4.901 44.884 68.713 1.00 86.77 C <BR>
HETATM 6640 C5 PLP A 500 5.327 43.248 66.794 1.00 91.55 C <BR>
HETATM 6641 C6 PLP A 500 6.014 42.124 66.269 1.00 92.40 C <BR>
HETATM 6642 C5A PLP A 500 4.287 43.977 65.936 1.00 92.05 C <BR>
HETATM 6643 O4P PLP A 500 4.919 44.983 65.137 1.00 91.48 O <BR>
HETATM 6644 P PLP A 500 3.850 45.746 64.212 0.40 89.98 P <BR>
HETATM 6645 O1P PLP A 500 2.942 46.559 65.059 1.00 90.28 O <BR>
HETATM 6646 O2P PLP A 500 3.052 44.763 63.428 1.00 89.69 O <BR>
HETATM 6647 O3P PLP A 500 4.581 46.636 63.284 1.00 90.10 O <BR>
HETATM 6663 O HOH 1 -2.199 65.598 27.605 1.00 37.63 O <BR>
HETATM 6664 O HOH 2 13.146 43.997 69.980 1.00 28.90 O <BR>
HETATM 6665 O HOH 3 3.514 34.147 84.461 1.00 40.65 O <BR>
HETATM 6666 O HOH 4 14.245 36.668 40.667 1.00 33.18 O <BR>
HETATM 6667 O HOH 5 6.748 58.168 71.500 1.00 37.09 O <BR>
HETATM 6668 O HOH 6 -3.541 20.765 51.638 1.00 34.79 O <BR>
HETATM 6669 O HOH 7 -4.102 61.235 21.691 1.00 38.94 O <BR>
HETATM 6670 O HOH 8 10.326 70.845 65.572 1.00 35.43 O <BR>
HETATM 6671 O HOH 9 -4.995 51.193 45.379 1.00 38.86 O <BR>
HETATM 6672 O HOH 10 -6.557 33.928 65.811 1.00 39.72 O <BR>
HETATM 6673 O HOH 11 -1.108 49.863 77.220 1.00 41.22 O <BR>
HETATM 6674 O HOH 12 -26.403 30.845 53.499 1.00 43.93 O <BR>
HETATM 6675 O HOH 13 -6.662 49.811 60.632 1.00 20.93 O <BR>
HETATM 6676 O HOH 14 0.524 46.344 51.157 1.00 30.77 O <BR>
HETATM 6677 O HOH 15 4.444 27.533 53.723 1.00 45.47 O <BR>
HETATM 6678 O HOH 16 -9.377 50.142 40.921 1.00 38.67 O <BR>
HETATM 6679 O HOH 17 16.732 42.270 53.224 1.00 43.17 O <BR>
HETATM 6680 O HOH 18 36.203 41.041 67.666 1.00 41.06 O <BR>
HETATM 6681 O HOH 19 -23.753 42.588 51.308 1.00 39.07 O <BR>
CONECT 2034 6639 <BR>
CONECT 5345 6654 <BR>
CONECT 6623 6624 6625 6626 6627 <BR>
CONECT 6624 6623 <BR>
CONECT 6625 6623 <BR>
CONECT 6626 6623 <BR>
CONECT 6627 6623 <BR>
CONECT 6628 6629 6630 6631 6632 <BR>
CONECT 6629 6628 <BR>
CONECT 6630 6628 <BR>
CONECT 6631 6628 <BR>
CONECT 6632 6628 <BR>
CONECT 6633 6634 6641 <BR>
CONECT 6634 6633 6635 6636 <BR>
CONECT 6635 6634 <BR>
CONECT 6636 6634 6637 6638 <BR>
CONECT 6637 6636 <BR>
CONECT 6638 6636 6639 6640 <BR>
CONECT 6639 2034 6638 <BR>
CONECT 6640 6638 6641 6642 <BR>
CONECT 6641 6633 6640 <BR>
CONECT 6642 6640 6643 <BR>
CONECT 6643 6642 6644 <BR>
CONECT 6644 6643 6645 6646 6647 <BR>
CONECT 6645 6644 <BR>
CONECT 6646 6644 <BR>
CONECT 6647 6644 <BR>
CONECT 6648 6649 6656 <BR>
CONECT 6649 6648 6650 6651 <BR>
CONECT 6650 6649 <BR>
CONECT 6651 6649 6652 6653 <BR>
CONECT 6652 6651 <BR>
CONECT 6653 6651 6654 6655 <BR>
CONECT 6654 5345 6653 <BR>
CONECT 6655 6653 6656 6657 <BR>
CONECT 6656 6648 6655 <BR>
CONECT 6657 6655 6658 <BR>
CONECT 6658 6657 6659 <BR>
CONECT 6659 6658 6660 6661 6662 <BR>
CONECT 6660 6659 <BR>
CONECT 6661 6659 <BR>
CONECT 6662 6659 <BR>
MASTER 342 0 4 47 25 0 0 6 6679 2 42 66 <BR>
END <BR>
II have made alignment in PIR using chain breaks "/" and block residues "." for SO4,PLP AND HOH.My alignment looks like this:<BR>
<BR>
<BR>
>P1;TvLDH<BR>
sequence:TvLDH: : : : ::: 0.00: 0.00<BR>
MRIYGEEHPNQQILSRIATNDGHGENSSYFDGWKAYEKDPFHLTDNPTGVIQMGLAENQL<BR>
SLDLIRDWMKKNPQASICTEEGVSEFKAIANFQDYHGLPTFRKAIAQFMEKVRGGRTRFD<BR>
PDRIVMSGGATGAQETIAFCLADPGEAFLIPTPYYPGFDR-FRWRTGVQLLPIHCHSSNK<BR>
FKITQAALETAYRKARNSHIRVKGILVTNPSNPLGTTMDRETLRTLVSFVNEKRMHLVCD<BR>
EIFSGTAFDKPSYVSVSEVIEDE--PYCDRDLIHIAYSLSKDLGVPGFRVGVIYSYNDAV<BR>
VSCARKMSSFGLVSSQTQHLLASMLGDEELTTSFLATSRTGLCGRRRVFTDGLKRVGIHC<BR>
LDGNAGLFCWMDLRPLLKEATVEAELRLWRVIINDVKLNISPGSSFHCSEPGWFRVCFAN<BR>
MDDTAMKIALRRIESFVYRENDAAVQAKNKRRWDEALRLSLPRRRFEDPTIMTPHLMSPH<BR>
SPLVQAAT/..*<BR>
>P1;TvLDH_model<BR>
structureX:TvLDH-loop:1 : :485 : ::: 0.00: 0.00<BR>
MRIYGEEHPNQQILSRIATNDGHGENSSYFDGWKAYEKDPFHLTDNPTGVIQMGLAENQL<BR>
SLDLIRDWMKKNPQASICTEEGVSEFKAIANFQDYHGLPTFRKAIAQFMEKVRGGRTRFD<BR>
PDRIVMSGGATGAQETIAFCLADPGEAFLIPTPYYPGFDR-FRWRTGVQLLPIHCHSSNK<BR>
FKITQAALETAYRKARNSHIRVKGILVTNPSNPLGTTMDRETLRTLVSFVNEKRMHLVCD<BR>
EIFSGTAFDKPSYVSVSEVIEDE--PYCDRDLIHIAYSLSKDLGVPGFRVGVIYSYNDAV<BR>
VSCARKMSSFGLVSSQTQHLLASMLGDEELTTSFLATSRTGLCGRRRVFTDGLKRVGIHC<BR>
LDGNAGLFCWMDLRPLLKEATVEAELRLWRVIINDVKLNISPGSSFHCSEPGWFRVCFAN<BR>
MDDTAMKIALRRIESFVYRENDAAVQAKNKRRWDEALRLSLPRRRFEDPTIMTPHLMSPH<BR>
SPLVQAAT/--*<BR>
>P1;1IAX<BR>
structureX:1IAX: 126 :A : 500 : :undefined:undefined:-1.00:-1.00<BR>
------------------------------------------------------------<BR>
------------------------------------------------------------<BR>
--------GATGANETIIFCLADPGDAFLVPSPYYPAFNRDLRWRTGVQLIPIHCESSNN<BR>
FKITSKAVKEAYENAQKSNIKVKGLILTNPSNPLGTTLDKDTLKSVLSFTNQHNIHLVCD<BR>
EIYAATVFDTPQFVSIAEILDEQEMTYCNKDLVHIVYSLSK-------------------<BR>
------------------------------------------------------------<BR>
------------------------------------------------------------<BR>
------------------------------------------------------------<BR>
--------/..*<BR>
<BR>
<BR>
Then I used advanced example as a template to write my input script:<BR>
<BR>
from modeller import *<BR>
from modeller.automodel import *<BR>
<BR>
class mymodel(automodel):<BR>
def special_restraints(self, aln):<BR>
rsr = self.restraints<BR>
for ids in (('NZ:278:A','C4A:500:A')):<BR>
<BR>
<BR>
atoms = [self.atoms[i] for i in ids]<BR>
rsr.add(forms.upper_bound(group=physical.upper_distance,<BR>
feature=features.distance(*atoms),<BR>
mean=3.5, stdev=0.1))<BR>
<BR>
env = environ()<BR>
env.io.hetatm = True<BR>
a = mymodel(env, alnfile='align-ligand.ali',<BR>
knowns=('TvLDH_model','1IAX'), sequence='TvLDH')<BR>
a.starting_model = 1<BR>
a.ending_model = 5<BR>
a.make()<BR>
<BR>
<BR>
then program starts calculating, and then I always get : <BR>
<BR>
<BR>
<BR>
<BR>
check_ali___> Checking pairwise structural superpositions. <BR>
<BR>
Equivalent CA pairs with distance difference larger than 6.0 angstroms:<BR>
<BR>
ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST<BR>
----------------------------------------------------<BR>
END OF TABLE<BR>
<BR>
check_ali___> Checking the sequence-structure alignment. <BR>
<BR>
Implied target CA(i)-CA(i+1) distances longer than 8.0 angstroms:<BR>
<BR>
ALN_POS TMPL RID1 RID2 NAM1 NAM2 DIST<BR>
----------------------------------------------<BR>
END OF TABLE<BR>
read_to_681_> topology.submodel read from topology file: 3<BR>
<BR>
getf_______W> RTF restraint not found in the atoms list:<BR>
residue type, indices: 17 485<BR>
atom names : C +N<BR>
atom indices : 3847 0<BR>
<BR>
getf_______W> RTF restraint not found in the atoms list:<BR>
residue type, indices: 17 485<BR>
atom names : C CA +N O<BR>
atom indices : 3847 3843 0 3848<BR>
<BR>
<BR>
fndatmi_285W> Only 153 residues out of 155 contain atoms of type CA<BR>
(This is usually caused by non-standard residues, such<BR>
as ligands, or by PDB files with missing atoms.)<BR>
mdtrsr__446W> A potential that relies on one protein is used, yet you have at<BR>
least one known structure available. MDT, not library, potential is used.<BR>
iup2crm_280W> No topology library in memory or assigning a BLK residue.<BR>
Default CHARMM atom type assigned: S --> S<BR>
This message is written only for the first such atom.<BR>
20 atoms in HETATM residues constrained<BR>
to protein CA atoms within 10.00 angstroms<BR>
20 atoms in residues without defined topology<BR>
constrained to be rigid bodies<BR>
indxatm_278E> No ":" in ATOM:RESID[:CHAINID] atom identifier: N<BR>
<BR>
<BR>
<BR>
but when I used model-ligand.py command it generate model including ligands successfully.<BR>
So my questions are:<BR>
1. What am I doing wrong with model-multiple-hetero.py command?<BR>
2.how 2 solve this problem??<BR>
<BR>
What do you think? Thank you for your suggestions.Sorry for my bad english.<BR>
sanjay<BR>
<BR>
<BR>
<BR>
</P>
sanjay Kumar singh kolkata
<br>
Bose Institute
<br>
Department of Botany
<br>
Main Campus
<br>
93\1 A.P.C.Road
<br>
Kolkata 700 009
<br>
India<br><br>
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