Hello, Modeller:
I try to model the ligand into my model by following the example of "Tutorial-2: Modeling ligands in the binding site'. First, I use a template and one of my model to build a alignment of the two. Then manually change the alignment to add "/.." to the end of the structures and sequence in the alignment. And change the number of residues of the structure file in the alignment. I then do the modeling using the modified alignment. But I keep getting the error message:
modeller. error: check_a_337E> structure not read in
I have checked that the structure files are all in the right path. I don't understand that why Modeller can't read the structure. I notice that the program generated two structure files ( all with xxx_fit) after the alignment. But these "xxx_fit" structures do not include the ligand. If I use these "xxx_fit" structures, there is no error message saying that "structure not read in", instead, it complain that "One or more atoms absent from MODEL". Since there is no ligand residue in such "xxx_fit" files. And if I manually add the ligand residue into the "xxx_fit", again, the modeller can't read the structure anymore.
I have included the files used for modeling as attachments. I use mod 8v1.
Thank you for help!
Bo
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_aln.pos 10 20 30 40 50 60 1PQ2-2C8Ahem KLPPGPTPLPIIGNMLQIDVKDICKSFTNFSKVYGPVFTVYFGMNPIVVFHGYEAVKEALIDNG 2c17mul1 ---------------------HMHNNFFKLQKKYGPIYSVRMGTKTTVIVGHHQLAKEVLI-KK 2c17 ---------------------HMHNNFFKLQKKYGPIYSVRMGTKTTVIVGHHQLAKEVLI-KK _consrvd * * *** * * * ** **
_aln.pos 70 80 90 100 110 120 1PQ2-2C8Ahem EEFSGRGN--SPISQRITKGLGIISSNG-KRWKEIRRFSL-TTLRNFGMGKRSIEDRVQEEAHC 2c17mul1 GKDFSGRPQMATLDIASNNRKGIAFADSGAHWQLHRRLAMATFALFKDGDQKLEKIICQEISTL 2c17 GKDFSGRPQMATLDIASNNRKGIAFADSGAHWQLHRRLAMATFALFKDGDQKLEKIICQEISTL _consrvd ** * ** * **
_aln.pos 130 140 150 160 170 180 190 1PQ2-2C8Ahem LVEELRKTKASPCDPTFILGCAPCNVICSVVFQKRFDYKDQNFLTLMKRFNENFRILNSPWIQV 2c17mul1 CDMLATHN-GQSIDISFPVFVAVTNVISLICFNTSYKN----GDPELNVIQNYNEGIID--NLS 2c17 CDMLATHN-GQSIDISFPVFVAVTNVISLICFNTSYKN----GDPELNVIQNYNEGIID--NLS _consrvd * * * *** *
_aln.pos 200 210 220 230 240 250 1PQ2-2C8Ahem CNN------FPLLIDCFPGTHNKVLKNVALTRSYIREKVKEHQASLDVNNPRDFIDCFLIKMEQ 2c17mul1 KDSLVDLVPWLKIFP--NKTLEKLKSHVKIRNDLLNKILENYKEKFRS-DSITNMLDTLMQAKM 2c17 KDSLVDLVPWLKIFP--NKTLEKLKSHVKIRNDLLNKILENYKEKFRS-DSITNMLDTLMQAKM _consrvd * * * *
_aln.pos 260 270 280 290 300 310 320 1PQ2-2C8Ahem EKDNQKSEF-------NIENLVGTVADLFVAGTETTSTTLRYGLLLLLKHPEVTAKVQEEIDHV 2c17mul1 NSDNGNAGPDQDSELLSDNHILTTIGDIFGAGVETTTSVVKWTLAFLLHNPQVKKKLYEEIDQN 2c17 NSDNGNAGPDQDSELLSDNHILTTIGDIFGAGVETTTSVVKWTLAFLLHNPQVKKKLYEEIDQN _consrvd ** * * * ** *** * ** * * * ****
_aln.pos 330 340 350 360 370 380 1PQ2-2C8Ahem IGRHRSPCMQDRSH-MPYTDAVVHEIQRYSDLVPTGVPHAVTTDTKFRNYLIPKGTTIMALLTS 2c17mul1 VGFS-RTPTISDRNRLLLLEATIREVLRLRPVAPMLIPHKANVDSSIGEFAVDKGTEVIINLWA 2c17 VGFS-RTPTISDRNRLLLLEATIREVLRLRPVAPMLIPHKANVDSSIGEFAVDKGTEVIINLWA _consrvd * * * * * ** * *** *
_aln.pos 390 400 410 420 430 440 1PQ2-2C8Ahem VLHDDKEFPNPNIFDPGHFLDKNGNFKKSD----YFMPFSAGKRICAGEGLARMELFLFLTTIL 2c17mul1 LHHNEKEWHQPDQFMPERFLN--PAGTQLISPSVSYLPFGAGPRSCIGEILARQELFLIMAWLL 2c17 LHHNEKEWHQPDQFMPERFLN--PAGTQLISPSVSYLPFGAGPRSCIGEILARQELFLIMAWLL _consrvd * ** * * * ** ** ** * * ** *** **** *
_aln.pos 450 460 470 480 490 1PQ2-2C8Ahem QNFNLKSVDDLKNLNTTAVTKGIVSLPPSYQICFIPV-----/.. 2c17mul1 QRFDLEVPDDGQLPSLEGIP-KVVFLIDSFKVKIKVRQAWRE/-- 2c17 QRFDLEVPDDGQLPSLEGIP-KVVFLIDSFKVKIKVRQAWRE/.. _consrvd * * * ** * * *
Bo Yang wrote: > I try to model the ligand into my model by following the example of > "Tutorial-2: Modeling ligands in the binding site'. First, I use a > template and one of my model to build a alignment of the two. Then > manually change the alignment to add "/.." to the end of the structures > and sequence in the alignment. And change the number of residues of the > structure file in the alignment. I then do the modeling using the > modified alignment. But I keep getting the error message: > > modeller. error: check_a_337E> structure not read in
If you use Modeller 8v2 or later, you will get a printout of the sequence mismatch which will help you here. I ran your script and got:
read_te_290E> Number of residues in the alignment and pdb files are different: 465 464 For alignment entry: 1 1PQ2-2C8Ahem x (mismatch at alignment position 465) Alignment VTKGIVSLPPSYQICFIPV.. PDB VTKGIVSLPPSYQICFIPVh Match ********************
i.e. your alignment lists two BLK residues, but your PDB structure contains only one HETATM residue (a heme group). So just remove one '.' from your alignment file (both for the template and the target sequence). I would also suggest that you remove the chain break (/) since in your input PDB the ligand is in the same chain (A) as the amino acids, while the chain break would force your model to put the ligand in a separate chain.
Ben Webb, Modeller Caretaker
Dear Ben:
Thank you very much for your help.
I fixed the alignment as the way you suggested. This time, modeller did not complain the structure problem. It went though but stopped later. Here is the error message: -------- fndatmi_285W> Only 464 residues out of 463 contain atoms of type CA delete__442E> One or more atoms absent from MODEL: O: 454: C: 454: N: 455: CA: 455: omgdel__425W> Unselected all O C +N +CA dihedrals: 474 mdtrsr__446W> A potential that relies on one protein is used, yet you have at least one known structure available. MDT, not library, potential is used. iup2crm_280W> No topology library in memory or assigning a BLK residue. Default CHARMM atom type assigned: FE --> C This message is written only for the first such atom. add_res_442E> One or more atoms absent from MODEL: NH1:124 O1D:491
---------
I do not quite understand the error message. The ligand in the structure template is "heme". I am not sure if this is the problem. The atom restrains in my .py is based on the residue ID in the template. "NH1:124" is a Arg 124 in the template, "O1D: 491" is the heme ligand. I don't know which part is wrong. Why the modeller says that "one or more atoms absent from MODEL"?
I have included the log file as an attachment. Thank you for your advice!
Bo
Modeller Caretaker modeller-care@salilab.org wrote: Bo Yang wrote: > I try to model the ligand into my model by following the example of > "Tutorial-2: Modeling ligands in the binding site'. First, I use a > template and one of my model to build a alignment of the two. Then > manually change the alignment to add "/.." to the end of the structures > and sequence in the alignment. And change the number of residues of the > structure file in the alignment. I then do the modeling using the > modified alignment. But I keep getting the error message: > > modeller. error: check_a_337E> structure not read in
If you use Modeller 8v2 or later, you will get a printout of the sequence mismatch which will help you here. I ran your script and got:
read_te_290E> Number of residues in the alignment and pdb files are different: 465 464 For alignment entry: 1 1PQ2-2C8Ahem x (mismatch at alignment position 465) Alignment VTKGIVSLPPSYQICFIPV.. PDB VTKGIVSLPPSYQICFIPVh Match ********************
i.e. your alignment lists two BLK residues, but your PDB structure contains only one HETATM residue (a heme group). So just remove one '.' from your alignment file (both for the template and the target sequence). I would also suggest that you remove the chain break (/) since in your input PDB the ligand is in the same chain (A) as the amino acids, while the chain break would force your model to put the ligand in a separate chain.
Ben Webb, Modeller Caretaker
Bo Yang wrote: > I fixed the alignment as the way you suggested. This time, modeller did > not complain the structure problem. It went though but stopped later. > Here is the error message: > -------- > fndatmi_285W> Only 464 residues out of 463 contain atoms of > type CA > delete__442E> One or more atoms absent from MODEL: O: 454: C: 454: N: > 455: CA: 455: > omgdel__425W> Unselected all O C +N +CA dihedrals: 474 > mdtrsr__446W> A potential that relies on one protein is used, yet you > have at > least one known structure available. MDT, not library, > potential is used. > iup2crm_280W> No topology library in memory or assigning a BLK residue. > Default CHARMM atom type assigned: FE --> C > This message is written only for the first such atom. > add_res_442E> One or more atoms absent from MODEL: NH1:124 O1D:491 > > --------- > > I do not quite understand the error message. The ligand in the structure > template is "heme". I am not sure if this is the problem. The atom > restrains in my .py is based on the residue ID in the template. > "NH1:124" is a Arg 124 in the template, "O1D: 491" is the heme ligand. I > don't know which part is wrong. Why the modeller says that "one or more > atoms absent from MODEL"?
Atom and residue numbers and names in Modeller always refer to the target model, not the template. This is because template PDBs can have inconsistent numbering, there may be multiple templates for some parts of the sequence, and some model residues may not be aligned to any templates. You can view the initial model (.ini file) to see the numbering Modeller is using for the model.
Ben Webb, Modeller Caretaker
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Bo Yang -
Modeller Caretaker