- modeller_usage - salilab.org

problem with structures
by Marcin Hus 04 Jul '04

04 Jul '04

Dear Sir, We are starting work with Modeller on the base of "Comparative protein structure modeling with Modeller: A practical approach". We have a problem with work of the script 'compare.top'. We obtained the following message: pntdp___252E> increase MAXRES or gap penalties. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 When we removed 'MALIGN3D' command from the script it seems to work but execution of the next script 'align2d.top' looked as follows: Dynamically allocated memory at amaxseq [B,kB,MB]: 2200483 2148. 909 2.099 TOP_________> 2 2 READ_MODEL FILE = '1f88.pdb' openf5__224_> Open 11 OLD SEQUENTIAL 1f88.pdb Dynamically allocated memory at amaxbnd [B,kB,MB]: 12194587 11908. 776 11.630 openf5__224_> Open 11 OLD SEQUENTIAL 1f88.pdb rdatm___297_> Segments, residues, atoms: 2 643 5069 rdatm___298_> Segment: 1 1 A 1 A 2639 rdatm___298_> Segment: 2 1 B 1 B 2430 iatmcls_286W> MODEL atom not classified: ALA:OT1 ALA iatmcls_286W> MODEL atom not classified: ALA:OT2 ALA iatmcls_286W> MODEL atom not classified: ASN:OT1 ASN TOP_________> 3 3 SEQUENCE_TO_ALI ALIGN_CODES = '1f88A' TOP_________> 4 4 READ_ALIGNMENT FILE = 'korhum.ali', ALIGN_CODES = 'korh um; ', ADD_SEQUENCE = ON openf5__224_> Open 11 OLD SEQUENTIAL korhum.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 12227463 11940. 882 11.661 openf5__224_> Open 11 OLD SEQUENTIAL korhum.ali read_al_374_> Non-standard residue type,position,sequence: / 339 1 read_al_374_> Non-standard residue type,position,sequence: / 645 1 Read the alignment from file : korhum.ali Total number of alignment positions: 645 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 korhum 643 3 1f88A undefined TOP_________> 5 5 ALIGN2D Dynamically allocated memory at amaxbnd [B,kB,MB]: 24499233 23925. 031 23.364 align2d_276_> ALIGN_BLOCK changed to 1. pdbnam__217W> Filename for PDB code not found: 1f88A Directories: ./ Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 1 mkapsa__293W> No TOPOLOGY_LIB is in memory. Use READ_TOPOLOGY to read one. openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL6v2}/modlib//as1.sim.m at rdrrwgh_268_> Number of residue types: 20 dispers_247E> Internal error: 642 643 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 24499233 23925. 031 23.364 Starting time : 2004/06/21 10:13:11. 753 Closing time : 2004/06/21 10:13:15. 768 Total CPU time [seconds] : 3.92 Please suggest what we did wrong. Thank You. Marcin Hus Medical University in Lublin Poland

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2quest.: howto add restraints & rand_seed
by Sascha Tayefeh 04 Jul '04

04 Jul '04

Dear community, having searched the whole of the manual as well as past posts, I could find helpful contributions, so I'm trying to find help here. I'm facing to questions: 1. RESTRAINTS: I didn't get the idea of how to *ADD* restraints to those modeller makes itself. Actually, I didn't get the idea of how manually add restraints with modeller, at all (remark: I'm a Charmm-User). So here is what I want to do, maybe some could help me with a little script: I'd like to fix the coordinates of all atoms of a slice of residues (e.g. Res 10-23). All the rest of the restraints are supposed to be calculated by modeller. 2. RAND_SEED: Is there a way to define the random seed for the "CALL ROUTINE = 'model'" command? Thank you very much in advance -- S.Tayefeh

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Problem with PDB file
by Lucas Bleicher 30 Jun '04

30 Jun '04

Dear colleagues, I�m facing a problem with Modeller6, and although it seems to be a common one (I�ve seen similar requests in the list archives), I just couldn�t fix it reading the previous posts nor the FAQ. The PDB file I�m using as a template starts at residue 8 and ends at residue 315. So, my alignement is as follows: ======================================================= C; A sample alignment in the PIR format; used in tutorial >P1;1DKU structureX:1DKU:8 : :315 : :PRPP:bacilo: 1.90: 0.19 NLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGY ARQDRKARSREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLE--DIVIVSPDHGGVTRARKLADRLKAPIAIIDK RRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKK-IERFKQLSVGP LLAEAIIRVHEQQSVSYLFS----* >P1;HUMA sequence:HUMA:8 : :315 : :PRPP:Homo sapiens: 2.00:-1.00 NIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMELLIMINACKIASASRVTAVIPCFPY ARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHK ERKKANEVDRMVLVGDVKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDKMKHCSKIQVIDISM ILAEAIRRTHNGESVSYLFSHVPL* ======================================================= The .top file was directly edited from the example model-default.top, and is as follows: ====================================================== # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 2 # uncomment to produce a large log file SET ALNFILE = 'ALIN.pir' # alignment filename SET KNOWNS = '1DKU' # codes of the templates SET SEQUENCE = 'HUMA' # code of the target SET ATOM_FILES_DIRECTORY = '/mod6v2/examples/tutorial-model/' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling ===================================================== Both the alignement file "ALIN.pir" and PDB file "1DKU.pdb" are on the /mod6v2/examples/tutorial-model/ directory. But although the program actually opens this pdb file, it shows this message: rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 309 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Does anybody has any hint on how to fix this problem? Thanks in advance, Lucas Bleicher __________________________________ Do you Yahoo!? Read only the mail you want - Yahoo! Mail SpamGuard. http://promotions.yahoo.com/new_mail

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Re: [modeller_usage] optimization problem...
by Eric Feyfant 30 Jun '04

30 Jun '04

Hi; Yes you can do it. I you are sure about the interaction sites and the orientation, I will suggest you to build manually the complex and use the resulting model as template and build a new model. But this time use the "strongest" optimization routine (see the manual it is routine 3 or 1 I don't remember". Also depend on the result you may have to eliminate some restraint that may bias the final model. I hope it helps. Eric ------------------------------------ Eric Feyfant, Ph.D. Senior research Scientist Computational Chemistry Wyeth Research 200 Cambridge Park Drive Cambridge, MA 02140 tel: +1 617 665 5656 fax: +1 617 665 5682 email: efeyfant(a)wyeth.com >>> "Himanshu Grover" <hgrover_00(a)iiita.ac.in> 6/30/2004 8:04:44 AM >>> hi, being a new user, I am facing many problems with modeller. now consider a situation in which i want to model only one particular domain/protein in a protein-protein complex, since the structure for the other domain/protein is available, but then i want to optimize the binding region of the modelled domain taking into context, the other domain as well... is it possible that i use the optimization routine of modeller for the same, only after putting both the proteins of the complex into proper interacting/binding orientation, so that energy minimization can be performed taking into context the entire complex and not just the modelled part thanks, for helping out... sincerely. _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org http://salilab.org/mailman/listinfo/modeller_usage

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optimization problem...
by Himanshu Grover 30 Jun '04

30 Jun '04

hi, being a new user, I am facing many problems with modeller. now consider a situation in which i want to model only one particular domain/protein in a protein-protein complex, since the structure for the other domain/protein is available, but then i want to optimize the binding region of the modelled domain taking into context, the other domain as well... is it possible that i use the optimization routine of modeller for the same, only after putting both the proteins of the complex into proper interacting/binding orientation, so that energy minimization can be performed taking into context the entire complex and not just the modelled part thanks, for helping out... sincerely.

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modelling proteins with multiple chains...
by Himanshu Grover 28 Jun '04

28 Jun '04

hi, i need some help with modelling a protein comprised of multiple chains. Firstly, is it possible to model the entire protein in one go, or diff. chains need to be modelled separately... Secondly, I want to provide my own alignment with the template, and am not using modeller's alignment routine... if I have to model 2 chains of the protein together, how do I provide the alignment... as the chains might not be contiguous... Moreover, when I do so, the resultant structure of modeller sticks together the loose ends of the 2 chains, as if they were continuous strands. This affects the model at the ends of the chains...How do I tell that this is the first chain and that is the second?? thanks, your sincerely, himan

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Two templates
by Han Choe 25 Jun '04

25 Jun '04

Dear all, I'm trying to model a protein structure using two homologous proteins as templates. I wonder how much the two known structures should be close for the modeling because I get errors like the following, stdevs__397E> STDEV < 0: -0.3487 Set to 1E-5. When I used the two known structures separately one by one, the modeling worked fine. Cheers, Han

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too slow...
by noha lim 24 Jun '04

24 Jun '04

Dear all, I just started using modeller a few weeks ago. And now I'm doing an example(seq_search.top) in the website. But it takes so long time(about 3 hours). And I think that's right, because in the seq_search.log file from website it also took 2 hours. Then why is it so slow? Others(like BLAST or something) take only a few seconds to find sequences. What are the big differences?? Thank you!! Noha Lim _________________________________________________________________ FREE pop-up blocking with the new MSN Toolbar get it now! http://toolbar.msn.click-url.com/go/onm00200415ave/direct/01/

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some food for thought...
by Himanshu Grover 23 Jun '04

23 Jun '04

Hullo, am a novice user of modeller... need some help for a problem described below... my target protein contains 2 chains which need to be modelled. I am currently modelling them independently and then concatenating their pdbs to get the complete protein. Firstly, is is possible to model the 2 chains together, rather than independently, since that would mean taking one chain into context while modelling the other... Secondly, after generating the protein, i need to check its binding to another protein, with which it is always found complexed. For instance, in case of immunoglobulins, we have 2 chains to be modelled, and then these chains are always found complexed with a peptide-MHC... So I need that the optimization of the chains and loop refinement of the heavy and the light chains should take place taking into consideration the peptide-MHC as well. The reason i want to do this is that I tried to generate the structure of some xyz protein through modeller, whose crystallographic structure is also available. so i took xyz(crystallographic) as the template and tried to generate the same structure with modeller. the new struc. has an rmsd value of 0.19 as compared to the actual structure, which is quite good. however, at the binding site, there are some side chains that are not nicely fitting on top of the actual structure. and some interactions have gone down, resulting in poor binding. is there a way to rectify this problem?? i was thinking of doing the simulated annealing part taking into context the entire complex... that is, say, after we concatenate the light and heavy chain of immunoglobulin with p-MHC, and then applying molecular dynamics taking into consideration p-MHC also...but am not sure whether that is possible or not... any say?? sincerely, himan...

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Optimization/Refinement of Models
by Cvetan Stojkoski 22 Jun '04

22 Jun '04

Hey list, I'm doing automated modelling of 800+ targets based on 31 templates. 10 structures are produced for each target. Below are the scores (objective function, procheck) for 10 structures of one of the targets. struct obj func core allow gener disall 1 303.8717 88.20% 11.80% 0.00% 0.00% 2 328.9031 96.10% 3.90% 0.00% 0.00% 3 373.319 88.20% 9.80% 2.00% 0.00% 4 350.9386 94.10% 2.00% 3.90% 0.00% 5 337.4741 90.20% 7.80% 0.00% 2.00% 6 335.0486 90.20% 5.90% 3.90% 0.00% 7 329.6535 96.10% 2.00% 2.00% 0.00% 8 298.5056 96.10% 2.00% 0.00% 2.00% 9 319.118 92.20% 5.90% 2.00% 0.00% 10 333.3913 88.20% 11.80% 0.00% 0.00% I tried to optimize the refinement of the models and theoretically get better structures. To this end I changed the following parameters: SET LIBRARY_SCHEDULE = 1 SET MAX_VAR_ITERATIONS = 500 SET MD_LEVEL = 'refine_5' SET REFINE_HOT_ONLY = 0 SET RSTRS_REFINED = 2 SET REPEAT_OPTIMIZATION = 5 SET MAX_MOLPDF = 1E6 Although the calculations took a lot longer, I did not end up with better structures as indicated by the following scores: struct obj func core allow gener disall 1 773.4081 80.40% 9.80% 7.80% 2.00% 2 973.659 76.50% 7.80% 7.80% 7.80% 3 1356.805 76.50% 9.80% 9.80% 3.90% 4 1084.465 72.50% 15.70% 9.80% 2.00% 5 1073.4241 66.70% 13.70% 9.80% 9.80% 6 1287.894 74.50% 11.80% 7.80% 5.90% 7 823.8506 82.40% 5.90% 11.80% 0.00% 8 1074.581 74.50% 17.60% 7.80% 0.00% 9 909.5347 78.40% 13.70% 5.90% 2.00% 10 1129.2293 80.40% 11.80% 3.90% 3.90% Is it that refine_5 is not particularly good or is it a combination of the variables that is leading to poor final structures? I would be pleased if somebody could recommend more appropriate parameters for optimizing/refining models. I have also tried doing external refinement in CNS. However, without any restraints to pass to CNS, the calculations lead to the loss of secondary structure. I have been comparing the restraint file formats used by MODELLER and CNS. It is not entirely clear to a CNS novice such as myself how one would go about converting a MODELLER formatted restraint file to a CNS acceptable one. Has anybody else looked into this or can recommend another method for external refinement? Many thanks, Cvetan

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