- modeller_usage - salilab.org

Modeller vs Prime or MOE
by Stradella, Omar 13 Nov '04

13 Nov '04

Are there any experienced users of Modeller out there that have tried other homology modeling software like Prime from Schrodinger or MOE from the Chemical Computing Group ?. Experiences, pros and cons ? Thanks Omar Stradella This e-mail, including any attachments, is a confidential business communication, and may contain information that is confidential, proprietary and/or privileged. This e-mail is intended only for the individual(s) to whom it is addressed, and may not be saved, copied, printed, disclosed or used by anyone else. If you are not the(an) intended recipient, please immediately delete this e-mail from your computer system and notify the sender. Thank you.

2 1

(senza oggetto)
by Matthias Negri 10 Nov '04

10 Nov '04

I wondered whether it's possible to build a DNA complex model? (My model is a heterodimer, bounded as a dimer on the DNA!) I'm sure it is, but i can't figure out which protocol i have to define.. Any tip or hint would be very appreciated.. Thanks Matthias Negri Univesity of Bologna

1 0

basic example erros
by butheryin 05 Nov '04

05 Nov '04

Hi, Modeller users I had tried to run the example 1 in workshop of the web site.but it reported lots of erros as follows on p4 win2k sp2 patch : mod7v7 seq_search.top Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2004/11/05 15:41:50.484 rdpir___223E> Array too small. Increase MAXRES current maximum, current need: 0 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 4784113 4671.985 4.562 Starting time : 2004/11/05 15:41:50.484 Closing time : 2004/11/05 15:41:51.437 Total CPU time [seconds] : 0.95 mod7v7 align.top Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2004/11/05 15:38:00.015 fullfn__230E> File not found: align.top Directories: :${MODINSTALL7v7}/bin\ Extensions : .top: Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 56755 55.425 0.054 Starting time : 2004/11/05 15:38:00.015 Closing time : 2004/11/05 15:38:00.937 Total CPU time [seconds] : 0.92 mod7v7 TvLDH-4mdh.top Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2004/11/05 15:40:15.625 fullfn__230E> File not found: TvLDH-4mdh.top Directories: :${MODINSTALL7v7}/bin\ Extensions : .top: Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 56755 55.425 0.054 Starting time : 2004/11/05 15:40:15.625 Closing time : 2004/11/05 15:40:16.562 Total CPU time [seconds] : 0.94 mod7v7 model-single.top Date and time of compilation : 09/13/2004 17:17:22 Job starting time (YY/MM/DD HH:MM:SS): 2004/11/05 15:40:44.375 check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 5436769 5309.345 5.185 Starting time : 2004/11/05 15:40:44.375 Closing time : 2004/11/05 15:40:45.625 Total CPU time [seconds] : 1.25

2 1

Helix Packing:Docking?
by David Piper 05 Nov '04

05 Nov '04

Modellers, I would like to add a single helix to an existing model. I have a set of distance restraints to orient residues on the helix to be added to the existing model. What sort of approach might be recommended here? Should I simply build a the additional helix ab initio, and then remodel the existing model + added helix based on the existing model + the built helix and distance restraints? Is there a way to simply add the new helix to the existing model by addition + distance restraints? Thanks, David

1 0

Merge twp alignment files
by HYUN CHUL KIM 04 Nov '04

04 Nov '04

Hi, all I made two alignment files with a threading program other than MODELLER. How can I merge these two alignment files? Each alignment file containts one query sequence and one template sequence. Query sequences from two alignment files are same to each other and have different gaps. Following sequences and gaps are made randomly. file1: 1aaab.ali >P1;source sequence: query : 1: : 700: : target sequence: unknown: : MASNMLDS--------KFLDKLDFJLSDKFLKDFLSJFDLJFLKDJFLDKFLS* >P1;1aaab structure: 1aaab: 100: B : 800: B: template: known structure: : M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDSAD--------* file2: 1bbbc.ali >P1;source sequence: query : 1: : 700: : target sequence: unknown: : MASNMLDSKFLDKLDFJLSDKFLKD----------FLSJFDLJFLKDJFLDKFLS* >P1;1bbbc structure: 1bbbc : 40: C : 700: C : template: known structure: : M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDSAD----------* ******MY TARGET ALIGNMENT FORM********************* >P1;source sequence: query : 1: : 700: : target sequence: unknown: : MASNMLDSKF---LDKLDFJLSDKFLKD--FLSJFDLJFLKDJFLDKFLS* >P1;1aaab structure: 1aaab: 100: B : 800: B: template: known structure: : M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDSAD-----* >P1;1bbbc structure: 1bbbc : 40: C : 700: C : template: known structure: : M-ASDFSAFDSADFSAFSDFSADFSAFSAD--ASDFASFDS-----AD* ****************************************************** Sincerely, Kim

2 1

Unknown residue type,position,sequence......
by 서주현 04 Nov '04

04 Nov '04

2 1

RE: [modeller_usage] Frustrating simple problem!
by Joel Tyndall 01 Nov '04

01 Nov '04

Hi folks, added to the errors pointed out by asmat (thanks for that), there was a break in the protein chain which I hadn't picked up. Thanks Joel -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Ph +64 3 4797293 Fax +64 3 4797034

1 0

Frustrating simple problem!
by Joel Tyndall 31 Oct '04

31 Oct '04

Hi folks, I've got a frustrating problem when I try to run a modeller job. I know it works as I've used it previously. I have seen the error before on the bulletin board but can't find the cause of my problem. I get the error: read_al_375E> Unknown residue type,position,sequence: 1 1 I don't have any alt conformations. any help would be great. I have attached the top and ali files. Cheers J -- Joel Tyndall, PhD Lecturer National School of Pharmacy University of Otago PO Box 913 Dunedin New Zealand Ph +64 3 4797293 Fax +64 3 4797034 >P1;UP_ecoli structureX:1rxc:1 : :253 : :unknown:unknown:-1.00:-1.00 MSKSDVFHLGLTKN------DLQGATLAIVPGDPDRVEKIAALMDKPVKLAS-HREFTTW RAELD------GKPVIVCSTGIGGPSTSIAVEELAQLG------IRTFLRIGTTGAIQPH INVGDVLVTTASVR------LDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHVGV TASSDTFYPGQERYD-TYSGRVVRHFKGSMEEWQAMGVMNYEMESATLLTMCASQGLRAG MVAGVIVNRTQQEIPN--AETMKQTESHAVKIVVEAARRLL* >P1;1uph sequence:uph:1 : :282 : :unknown:unknown:-1.00:-1.00 MKEDILYHFNLTTSRHNFPALFGDVKFVCVGGSPSRMKAFIRCVGAELGLDCPGRDYPNI CAGTDRYAMYKVGPVLSVSHGMGIPSISIMLHELIKLLYYARCSNVTIIRIGTSGGIG-- LEPGTVVITEQAVDTCFKAEFEQIVLGKRVIRKTDLNKKLVQELLLCSAELSEFTTVVGN TMCTLDFYEGQGRLDGALCSYTEKDKQAYLEAAYAAGVRNIEMESSVFAAMCSACGLQAA VVCVTLLNRLEGDQISSPRNVLSEYQQRPQRLVSYFIKKKL* 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 allroy.otago.ac.nz 2.6.5-1.358smp x86_64 Date and time of compilation : 07/16/2002 11:42:16 Job starting time (YY/MM/DD HH:MM:SS): 2004/10/29 16:08:43.499 TOP_________> 106 706 SET ALNFILE = 'UP_human_ecoli' TOP_________> 107 707 SET KNOWNS = '1rxc_mono' TOP_________> 108 708 SET MD_LEVEL = 'refine_3' TOP_________> 109 709 SET SEQUENCE = '1uph' TOP_________> 110 710 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 111 711 SET OUTPUT_DIRECTORY = './' TOP_________> 112 712 SET PDB_EXT = '.pdb' TOP_________> 113 713 SET ALIGNMENT_FORMAT = 'PIR' TOP_________> 114 714 SET STARTING_MODEL = 1 TOP_________> 115 715 SET ENDING_MODEL = 5 TOP_________> 116 716 SET DEVIATION = 4.000000 TOP_________> 117 717 SET FINAL_MALIGN3D = 1 TOP_________> 118 718 SET DO_LOOPS = 1 TOP_________> 119 719 SET RADII_FACTOR = 0.915 TOP_________> 120 720 SET LOOP_STARTING_MODEL = 1 TOP_________> 121 721 SET LOOP_ENDING_MODEL = 5 TOP_________> 122 722 SET LOOP_MD_LEVEL = 'refine_2' TOP_________> 123 723 CALL ROUTINE = 'model' TOP_________> 124 399 CALL ROUTINE = 'getnames' TOP_________> 125 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 126 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 127 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 128 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 129 513 SET ROOT_NAME = SEQUENCE TOP_________> 130 514 RETURN TOP_________> 131 400 CALL ROUTINE = 'homcsr' TOP_________> 132 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153.583 2.103 openf5__224_> Open 11 OLD SEQUENTIAL UP_human_ecoli.ali Dynamically allocated memory at amaxbnd [B,kB,MB]: 6262261 6115.489 5.972 openf5__224_> Open 11 OLD SEQUENTIAL UP_human_ecoli.ali read_al_375E> Unknown residue type,position,sequence: 1 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 6262261 6115.489 5.972 Starting time : 2004/10/29 16:08:43.499 Closing time : 2004/10/29 16:08:44.900 Total CPU time [seconds] : 1.38 INCLUDE # remove all the #'d bits. TOP FILE FOR EXTENSIVE REFINEMENT SET INITIAL_MALIGN3D = 1 # don't worry about this. SET OUTPUT_CONTROL = 1 1 1 1 1 # don't worry about this either SET ALNFILE = 'UP_human_ecoli' # alignment file, worry about this SET KNOWNS = '1rxc_mono' # refers to xtal name in algnmnt SET MD_LEVEL = 'refine_3' # sets simulated annealing level 1 high 3 low. 3 good to tansfer coords and fix major gliches. SET SEQUENCE = '1uph' # name of target seq in pir file SET ATOM_FILES_DIRECTORY = './:../atom_files' # for modeller use. It will tell you if it can't find its atoms. SET OUTPUT_DIRECTORY = './' # is exactly that; can alter this SET PDB_EXT = '.pdb' # leave all structures as this SET ALIGNMENT_FORMAT = 'PIR' # leave it this way; easier SET STARTING_MODEL = 1 # these two define the number of SET ENDING_MODEL = 5 # models to build. Unclear why it is this way SET DEVIATION = 4.000000 # defines how much variation is tolerated when building your model from the randomised coords. Leave as is. SET FINAL_MALIGN3D = 1 # don't worry about this SET DO_LOOPS = 1 # for explicit loop building SET RADII_FACTOR = 0.915 # the x factor for good structure. Always include this. SET LOOP_STARTING_MODEL = 1 #back to explicit loop modeling SET LOOP_ENDING_MODEL = 5 # i built 10 per model, 50 loops in total. Too much. 1 model 10 loops SET LOOP_MD_LEVEL = 'refine_2' # md level used; same as above CALL ROUTINE = 'model' # is the modeller key word for modelling building

1 0

where to put the ligand?
by Youbin Tu 27 Oct '04

27 Oct '04

Hi all: Thanks for Alicia and Modeler taker's kind hlep last time. Here come some new questions. Basically I just want to build a homology model complexed with an additional ligand. This time, I created a small molecule(ethane) to test whether the method works. First,In InsightII, I built ethane and optimized using cvff ( the program did not allow me to use charmm22 at that time.) and output it as an RTF file in charmm22 force field.- Second, I did some modification to some of the library files: 1. append part of the content of RTF file to the end of top_allh.lib and top_heav.lib 2. add an entry to restyp.lib, use j as the one letter abbreviation. (142 | ETH | j | ETHL | ethyl ) Third, alignment was modified so that "j' was appended to the end of the target sequence and '-' was used in the relative position of the template sequence. The program worked well with the above changes, but I could not see any ligand shown in the created pdb file! I could see heme was shown as the 513th residue but no ethane was shown as the 514th residue! Here I attached the ali file,wish you can give me some suggestions. Again, I would like to ask whether it is correct for me to just put any ligand at the end of the target sequence in the alignment file? Is it necessary to create the restraint file when some ligands are introduced? If fact, in the above test, I just want to see the ligand are really in the final model, and I do not mind where is it? So, anyone can tell me how to make the ligand appear in the final model? youbin

1 0

Protein with uracil
by Michel Seigneuret 27 Oct '04

27 Oct '04

Dear Collègues, I am trying to model a protein with a bound uracil. I have a template also with bound uracil. I modified the testyp.lib file in order to name uracil "U" and I included /U* at the end of the alignment for both template and target. The modeling goes on smoothly but I get a strange uracil with protein backbone atoms: N, CA, C,... Therefore Modeller thinks U is an aminoacid. I tried various tricks: putting different chain names for the protein and the uracil in the template pdb file, or changing ATOM to HETATM for the uracil, adding HETATM_IO = on to the top file but the problem remains. Could you please help me ? Two more things: I still use Modeller 6v2. I am not currently a subscriber to the list, therefore please answer directly to me and/or send the message to the list if you think it is worth it. Thanks in advance; Michel Michel Seigneuret Institut Cochin, U567-UMR8104 Département de Biologie Cellulaire 22 rue Méchain, 75014 Paris, France Tel: 33 (0)1 40 51 64 50 Fax: 33 (0)1 40 51 64 54

2 1