- modeller_usage - salilab.org

How to avoid funny structure in all-hydrogen modeling?
by Lesheng Kong 26 Aug '02

26 Aug '02

Dear all, Have anyone ever generated all-hydrogen models? For all-hydrogen modeling, the generated models always have some funny structures(such as one hydrogen atom is connected with several other atoms. I think some maybe due to bad contact, but some bond lengths are longer than 2.5 angstrom). These funny connections sometimes appear in ARG and SER. Is it possible because models have not been thoroughly refined? I have tried to set MODELLER "MD_LEVEL" to "refine_1" (# very thorough MD optimization), but no effects. How to avoid or remove these funny structures in all-hydrogen modeling? Thank you very much for your kind help! With best regards, Kong Lesheng

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OPTIMIZE
by Bozidar Yerkovich 26 Aug '02

26 Aug '02

from Alex: Dear all, I would like to optimize a protein model using molecular dynamics approach, but I have a problem with choosing of parameters for OPTIMIZE command (MD_TIME_STEP, MAX_ITERATIONS, TEMPERATURE etc). Does anybody know a suitable MD script for model optimization in Modeler 6.2? Thank you very much for your kind help! With best regards, Alex Bazilevsky ------------------------------ Alex Bazilevsky PhD student Protein Engineering Departmant Institute of Molecular Biology & Genetics 150 Acad. Zabolotnogo Street Kiev, 03143, Ukraine Tel.: 38 044 266-5589, Fax: 38 044 266-0759 E-mail: alextk(a)univ.kiev.ua

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anti-hCG IgG1 structure
by zjnjuct 23 Aug '02

23 Aug '02

Hi, Is there anybody know the all-atom structure of anti-hCG (IgG1)? We know, only three whole structures of antibodies are available. Two of their PDB codes are 1IGT, 1IGY, for IgG2a and IgG1. However, they are anti-phenobarbital for 1IGY, as mouse IgG1. The complex between anti-hCG and hCG found is 1QFW. Only Fv fragment of anti-hCG is present in the structure. Now, we 'd like to know the whole structure for anti-hCG. Is there any method to combine the 1IGY and 1QFW to get the new structure for anti-hCG? Thank you very much. Jian __________________________________________________ Do You Yahoo!? Yahoo! Finance - Get real-time stock quotes http://finance.yahoo.com

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how are these restraints obtained?
by michael hanlon (BITS) 21 Aug '02

21 Aug '02

Hi folks, I am looking at some of the examples provided in the supplementary material, and in particular inclusion of user specified restraints. My question is (i) how are these restraints obtained, (ii) what do the numbers (i.e. RESTRAINT_PARAMETERS)actually refer to. I've looked at the manual but am not much the wiser. Here's the script: -------------------------------------------------------------------------------- INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ATOM_FILES_DIRECTORY = '/usr/users/hanlon/Modeller/modeller6v1/atom_files' SET ALNFILE = 'TvLDH-4mdh-1emd_ed.ali' SET KNOWNS = '4mdhA' '1emd_ed' SET SEQUENCE = 'TvLDH' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 SET HETATM_IO = on CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'special_restraints' #ADD_RESTRAINT ATOM_IDS = 'NH1:161' 'O1A:335',; # RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1 #ADD_RESTRAINT ATOM_IDS = 'NH2:161' 'O1B:335',; # RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1 #ADD_RESTRAINT ATOM_IDS = 'NE2:186' 'O2:335',; # RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1 ADD_RESTRAINT ATOM_IDS = 'NH1:161' 'O1A:334',; RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1 ADD_RESTRAINT ATOM_IDS = 'NH2:161' 'O1B:334',; RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1 ADD_RESTRAINT ATOM_IDS = 'NE2:186' 'O2:334',; RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1 RETURN END_SUBROUTINE --------------------------------------------------------------------------------] Any help much appreciated, Mike

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Alignment sequence not found in PDB file
by Karsten Suhre 16 Aug '02

16 Aug '02

Hi! when I get the following error message, I understand that the sequence in my PDB file does not correspond to that read from the alignment. Up to know, it was what had happened, and I always found the problem by trial and error, but this time .... :-( rdpir___648E> Alignment sequence not found in PDB file: 2 ./1EL3.pdb Is there some command or switch in modeller to get some more information on what the problem is? i.e. which amino acid does not match? Thank you very much for any hint, Karsten. PS: here my commands: SET OUTPUT_CONTROL = 1 1 1 1 0 READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES = 'all' and the output: Job starting time (YY/MM/DD HH:MM:SS): 2002/08/15 23:41:12.615 TOP_________> 2 2 READ_ALIGNMENT FILE = 'tcoffee.aln', ALIGN_CODES = 'all' openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb openf5__224_> Open 11 OLD SEQUENTIAL tcoffee.aln openf5__224_> Open 13 OLD SEQUENTIAL ./1EL3.pdb rdpir___648E> Alignment sequence not found in PDB file: 1 ./1EL3.pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 8065909 7876.864 7.692 PPS: Attached are the input files (there is only one sequence in the alignment including gaps .. and the PDB file does only contain ATOM lines. That's because I eliminated all other stuff to see whether the error changes .. it doesn't, and I compared the sequences between the PDB file and the alignment - they are identical). -- Karsten Suhre Charge de Recherche CNRS (Research Scientist) Information Genetique & Structurale UMR CNRS 1889 31, chemin Joseph Aiguier F-13402 Marseille Cedex 20 Tel: ++33.4.91.16.46.04 Sec: ++33.4.91.16.45.48 Fax: ++33.4.91.16.45.49 mailto:Karsten.Suhre@igs.cnrs-mrs.fr http://igs-server.cnrs-mrs.fr/~suhre

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Re: Re: "Array too small. Increase MBNDPF"
by Kong Lesheng 16 Aug '02

16 Aug '02

Dear Dr. Bozidar Yerkovich, Thank you very much for your kind help! I have solved this problem! :-) The error message is due to problems of my topology files format. I have modified the RTF file, and now I can generate models including HYP! My topology files for HYP as follows: RESI HYP 0.00000 GROUP ! HD1 HD2 ATOM N N -0.29 ! | \ / ATOM CA CP1 0.02 ! N---CD HG ATOM HA HB 0.09 ! | \ / ATOM CD CP3 0.18 ! | CG ATOM HD1 HB 0.00 ! | / \ ATOM HD2 HB 0.00 ! HA-CA--CB OG2--HG2 GROUP ! | / \ ATOM CB CP2 -0.18 ! | HB1 HB2 ATOM HB1 HA 0.09 ! O=C ATOM HB2 HA 0.09 ! | GROUP ATOM CG CT1 0.14 ATOM HG HA 0.09 ATOM OG2 OH1 -0.66 ATOM HG2 H 0.43 GROUP ATOM C CC 0.53 ATOM O O -0.53 BOND O C C CA C +N BOND N CA CA CB CB CG CG CD N CD CG OG2 BOND HA CA HG CG HG2 OG2 HD1 CD HD2 CD HB1 CB HB2 CB IMPR N -C CA CD IMPR C CA +N O IMPR CA N C CB DONOR HG2 OG2 ACCEPTOR O C IC CD N CA CB 1.4468 114.9587 -11.2918 101.8808 1.5360 IC CD N CA HA 1.4468 114.9587 -129.2290 110.5162 1.0924 IC CD N CA C 1.4468 114.9587 109.5875 111.6376 1.5380 IC HA CA N +C 1.0924 110.5162 50.0429 122.5076 1.3162 IC CD +C *N CA 1.4468 122.5296 -179.2170 122.5076 1.4550 IC CA N CD CG 1.4550 114.9587 -11.8599 102.4794 1.5305 IC CA N CD HD1 1.4550 114.9587 -131.8901 111.1069 1.0924 IC CA N CD HD2 1.4550 114.9587 106.0401 109.5406 1.0925 IC N CA CB CG 1.4550 101.8808 29.6080 103.6605 1.5362 IC N CA CB HB1 1.4550 101.8808 152.0681 112.9350 1.0925 IC N CA CB HB2 1.4550 101.8808 -86.5729 108.9663 1.0930 IC N CA C O 1.4550 111.6376 149.4002 120.4223 1.2316 IC N CA C N 1.4550 111.6376 -31.0428 120.0469 1.3161 IC N CA *C O 1.3161 120.0469 -179.5571 120.4223 1.2316 IC CA CB CG OG2 1.5360 103.6605 -158.7449 112.5784 1.4300 IC CA CB CG HG 1.5360 103.6605 79.0616 109.5554 1.0926 IC CD CG OG2 HG2 1.5305 112.2089 31.3937 109.5000 1.0300 IC N CD CG CB 1.4468 102.4794 29.9288 103.3139 1.5362 PATCHING FIRS PROP Thanks a lot! With best regards, Kong Lesheng --------------------------------- BioInformatics Center National University of Singapore 10 Kent Ridge Cresent Singapore119260 Tel: (65)6874 4459 Fax: (65)6778 2466 --------------------------------- ======= 2002-08-12 You write============== >I'll have to take a closer look at this. I'll let you know... >Best, >Bozidar > > >On Mon, 12 Aug 2002, Kong Lesheng wrote: > >> Dear Dr. Bozidar Yerkovich, >> I have added topology of HYP into top.lib, and modified restyp.lib(using "o" as residue code for HYP). >> But when I did modelling, it reported the following errors and warnings. >> addprm__223E> Array too small. Increase MBNDPF >> recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 >> getf_______W> RTF restraint not found in the atoms list: >> getf_______W> RTF restraint not found in the atoms list: >> getf_______W> RTF restraint not found in the atoms list: >> iatmcls_286W> MODEL atom not classified: ALA:OT1 ALA >> iatmcls_286W> MODEL atom not classified: ALA:OT2 ALA >> r_stere_607W> Cannot find params in params file: >> addprm__440W> Adding params (mean,force,period): 1.5431 300.0000 1 >> r_stere_607W> Cannot find params in params file: >> addprm__440W> Adding params (mean,force,period): 3.0698 300.0000 1 >> r_stere_607W> Cannot find params in params file: >> addprm__440W> Adding params (mean,force,period): 1.0924 300.0000 1 >> r_stere_607W> Cannot find params in params file: >> addprm__440W> Adding params (mean,force,period): 3.8828 300.0000 1 >> r_stere_607W> Cannot find params in params file: >> addprm__440W> Adding params (mean,force,period): 66.6866 60.0000 1 >> r_stere_607W> Cannot find params in params file: >> addprm__440W> Adding params (mean,force,period): 111.1069 60.0000 1 >> ....... >> >> How could I fix these problem? >> I attach an uuencoded compressed tar archive of all input and output files. >> Thank you very much! >> With best regards, >> Kong Lesheng >> >> --------------------------------- >> BioInformatics Center >> National University of Singapore >> 10 Kent Ridge Cresent >> Singapore119260 >> Tel: (65)6874 4459 >> Fax: (65)6778 2466 >> --------------------------------- >> >> > >. = = = = = = = = = = = = = = = = = = = =

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SS bridges
by Bozidar Yerkovich 14 Aug '02

14 Aug '02

>From Eric: Hi Pedro; You can tell modeller to make particular disulfide bridges using this sub routine: SUBROUTINE ROUTINE = 'special_patches' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '160: ' '190: ' # 160 is the cystein number on the sequence PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '122: ' '206: ' PATCH RESIDUE_TYPE = 'DISU', RESIDUE_IDS = '76: ' '128: ' RETURN END_SUBROUTINE Good luck Eric ------------------------------------ Dr Eric Feyfant Computational Chemist Departement of Biological Chemistry Wyeth Research 85 Bolton St. Cambridge, MA 02140 tel: +1 617 665 8987 fax: +1 617 665 8993 email: efeyfant(a)wyeth.com

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disulfide bridges
by Pedro A Reche 14 Aug '02

14 Aug '02

Hi all, I am modelling a protein that should have 3 disulfide bridges however the model I am getting does not shown them. Does any know how to tell modeller the cys pairs that are making disulfide bridges? Cheers, Pedro ******************************************************************* PEDRO A. RECHE , pHD TL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School, EM: reche(a)research.dfci.harvard.edu 44 Binney Street, D1510A, EM: reche(a)mifoundation.org Boston, MA 02115 URL: http://www.reche.org *******************************************************************

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problems with optimaze
by Pedro A Reche 14 Aug '02

14 Aug '02

Hi all, I am trying to optimaze a model by just running the follwing script: Example for: OPTIMIZE, SWITCH_TRACE # This will optimize stereochemistry of a given model, including # non-bonded contacts. READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib' READ_MODEL FILE = '1c11' SEQUENCE_TO_ALI ATOM_FILES = '1c11', ALIGN_CODES = '1c11' SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES '1c11.ini', ; ALIGN_CODES = ALIGN_CODES '1c11-ini' GENERATE_TOPOLOGY SEQUENCE = '1c11-ini' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off WRITE_MODEL FILE = '1c11.ini' # Generate the restraints: MAKE_RESTRAINTS RESTRAINT_TYPE = 'stereo' WRITE_RESTRAINTS FILE = '1c11.rsr' ENERGY DYNAMIC_SPHERE = on SWITCH_TRACE TRACE_OUTPUT = 1, FILE = '1c11.trc' OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20 OPTIMIZE OPTIMIZATION_METHOD = 3, TEMPERATURE = 300, MAX_ITERATIONS = 50 OPTIMIZE OPTIMIZATION_METHOD = 1, MAX_ITERATIONS = 20 ENERGY WRITE_MODEL FILE = '1c11.B' Unfortunally, I am getting the an error after running mod optimaze.top, and I do not see what is wrong, possble something silly but I do not wee where the problem is. So any help will be very welcomed. 1c11 is the name of the model. I moved Here it follows the optimaze.log 1c11.B99990001 to 1c11. MODELLER 6v2, 17 Feb 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux mif.dfci.harvard.edu 2.4.13 i686 Date and time of compilation : 05/24/2002 09:27:23 Job starting time (YY/MM/DD HH:MM:SS): 2002/08/13 12:19:52.681 rdactio_534E> Command not recognized: EXAMPLE FOR: OPTIMIZE, SWITCH_TRACE recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2190959 2139.608 2.089 Starting time : 2002/08/13 12:19:52.681 Closing time : 2002/08/13 12:19:54.367 Total CPU time [seconds] : 1.58 -- ******************************************************************* PEDRO A. RECHE , pHD TL: 617 632 3824 Dana-Farber Cancer Institute, FX: 617 632 4569 Harvard Medical School, EM: reche(a)research.dfci.harvard.edu 44 Binney Street, D1510A, EM: reche(a)mifoundation.org Boston, MA 02115 URL: http://www.reche.org *******************************************************************

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Error message
by Troy Wymore 13 Aug '02

13 Aug '02

Hello Modellers! I have an error message popping up and am not sure how to interpret. Here it is: delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 41972 38728 act10___551E> No such routine: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I have not updated my Modeller6 to Modeller6v2 yet. Maybe that's the problem. Any help is much appreciated. Troy Wymore Pittsburgh Supercomputing Center Biomedical Initiative Group

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