- modeller_usage - salilab.org

How to extract the backbone conformation alone from template?
by Nataraj Balkrishnan 11 Apr '04

11 Apr '04

Dear modellers, For my modelling process, I want to extract backbone conformation alone from the template to the target model.I mean,I want to restrict transformation of side chain to target model. Is it possible to achieve this in automatic modelling routine as given in "/example/tutorial-model/model-default.top" file. Otherwise may I have to write lengthier top file script to prevent this sidechain transformation from template to target? reply with example top script will be hightly appreciated. Let me know ... Thank you inadvance. Yours truly, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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karthik.
by kambhampati anjaneyulu 11 Apr '04

11 Apr '04

sir when i run modeller .it is showing error .how to run the modeller successfully 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, Windows_NT SSEDS x86 Family 15 Model 1 Stepping 3, GenuineIn Date and time of compilation : Jul 09 2002 16:21:30 Job starting time (YY/MM/DD HH:MM:SS): 2004/04/10 19:43:40.686 TOP_________> 105 705 SET ALNFILE = 'dd.ali' TOP_________> 106 706 SET KNOWNS = '1FFT' TOP_________> 107 707 SET SEQUENCE = '1EKH' TOP_________> 108 708 SET ATOM_FILES_DIRECTORY = './:../atom_files' TOP_________> 109 709 SET STARTING_MODEL = 1 TOP_________> 110 710 SET ENDING_MODEL = 1 TOP_________> 111 711 CALL ROUTINE = 'model' TOP_________> 112 399 CALL ROUTINE = 'getnames' TOP_________> 113 509 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATI ON; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 114 510 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERA TI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 115 511 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 116 512 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 117 513 SET ROOT_NAME = SEQUENCE TOP_________> 118 514 RETURN TOP_________> 119 400 CALL ROUTINE = 'homcsr' TOP_________> 120 106 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQ UE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 2205269 2153. 583 2.103 fullfn__230E> File not found: dd.ali Directories: Extensions : :.ali Prefixes : nothing, pdb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2205269 2153. 583 2.103 Starting time : 2004/04/10 19:43:40. 686 Closing time : 2004/04/10 19:43:42. 530 Total CPU time [seconds] : 1.72 --------------------------------- Do you Yahoo!? Yahoo! Tax Center - File online by April 15th

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Re: [modeller_usage] residue problem
by Eric Feyfant 07 Apr '04

07 Apr '04

Hermant; Extract your sequence from the pdb file and your problem will be solved. Eric >>> hemant kushwaha <ritturajhemant(a)yahoo.com> 4/7/2004 10:00:58 AM >>> respected sir, I am having a problem that my alignment file has some residues missing than in the pdb file. Therefore modeller is giving the following error: Read the alignment from file : alignmenttest.ali Total number of alignment positions: 970 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1BDG 440 1 1BDG undefined 2 1DGK 898 1 1DGK undefined 3 1CZA 898 1 1CZA undefined 4 1BG3 887 1 1BG3 undefined 5 1HKC 896 1 1HKC undefined 6 1IG8 458 1 1IG8 undefined 7 1Str 493 1 1Str Candida albicans TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1BDG.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 1 1 10 LEU 14 GLN -----LFEKVV rdabrk__288W> Protein not accepted: 1 openf5__224_> Open 11 OLD SEQUENTIAL ./1DGK.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./1CZA.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./1BG3.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 4 1 3 ASP 11 MET -----DDQVKK rdabrk__288W> Protein not accepted: 4 openf5__224_> Open 11 OLD SEQUENTIAL ./1HKC.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 5 1 18 VAL 3 ASP -----VKKIDK rdabrk__288W> Protein not accepted: 5 openf5__224_> Open 11 OLD SEQUENTIAL ./1IG8.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 6 1 9 LYS 12 ASN -----KELMQQ rdabrk__288W> Protein not accepted: 6 check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 How can this problem be solved, that modeller should read pdb file with respect to residue position in alignment regards hemant __________________________________ Do you Yahoo!? Yahoo! Small Business $15K Web Design Giveaway http://promotions.yahoo.com/design_giveaway/ _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org http://salilab.org/mailman/listinfo/modeller_usage

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residue problem
by hemant kushwaha 07 Apr '04

07 Apr '04

respected sir, I am having a problem that my alignment file has some residues missing than in the pdb file. Therefore modeller is giving the following error: Read the alignment from file : alignmenttest.ali Total number of alignment positions: 970 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1BDG 440 1 1BDG undefined 2 1DGK 898 1 1DGK undefined 3 1CZA 898 1 1CZA undefined 4 1BG3 887 1 1BG3 undefined 5 1HKC 896 1 1HKC undefined 6 1IG8 458 1 1IG8 undefined 7 1Str 493 1 1Str Candida albicans TOP_________> 121 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL ./1BDG.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 1 1 10 LEU 14 GLN -----LFEKVV rdabrk__288W> Protein not accepted: 1 openf5__224_> Open 11 OLD SEQUENTIAL ./1DGK.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./1CZA.pdb openf5__224_> Open 11 OLD SEQUENTIAL ./1BG3.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 4 1 3 ASP 11 MET -----DDQVKK rdabrk__288W> Protein not accepted: 4 openf5__224_> Open 11 OLD SEQUENTIAL ./1HKC.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 5 1 18 VAL 3 ASP -----VKKIDK rdabrk__288W> Protein not accepted: 5 openf5__224_> Open 11 OLD SEQUENTIAL ./1IG8.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 6 1 9 LYS 12 ASN -----KELMQQ rdabrk__288W> Protein not accepted: 6 check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 How can this problem be solved, that modeller should read pdb file with respect to residue position in alignment regards hemant __________________________________ Do you Yahoo!? Yahoo! Small Business $15K Web Design Giveaway http://promotions.yahoo.com/design_giveaway/

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Modeller crashed due to heavy load.....!
by Nataraj Balkrishnan 02 Apr '04

02 Apr '04

Dear Modellelers, I tried to model my target from 12 templates, At the middle of the modeller run , the program crashed suddently and reported the following message at the terminal window itself. I suspect,crash might have been due to modeling from 12 templates(I mean modeller find it overload above its capability) or whether it is a bug ? Kindly help me.(I am using Modeller6v2 of windows version) C:\modeller6v2\NDALI>c:\modeller6v2\bin\modeller6v2 model-default 1>mod el-default.log forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Re ad Image PC Routine Line Source modeller6v2.exe 00630729 Unknown Unknown Unknown modeller6v2.exe 00630587 Unknown Unknown Unknown modeller6v2.exe 0062F764 Unknown Unknown Unknown modeller6v2.exe 0062FB99 Unknown Unknown Unknown modeller6v2.exe 00626EFE Unknown Unknown Unknown modeller6v2.exe 00509EAA Unknown Unknown Unknown modeller6v2.exe 00484FC7 Unknown Unknown Unknown modeller6v2.exe 004412AA Unknown Unknown Unknown modeller6v2.exe 005EF888 Unknown Unknown Unknown modeller6v2.exe 005441D8 Unknown Unknown Unknown modeller6v2.exe 004CF8EC Unknown Unknown Unknown modeller6v2.exe 00657929 Unknown Unknown Unknown modeller6v2.exe 0064A144 Unknown Unknown Unknown KERNEL32.dll 77E87903 Unknown Unknown Unknown C:\modeller6v2\NDALI> Thank you , Yours truly, B.Nataraj --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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Modelling of one conformation, docking another being a problem?
by Nataraj Balkrishnan 01 Apr '04

01 Apr '04

Dear modellers, I have modelled protein(Transmembrane protein) from a template,whose conformation avilable in closed state. But from litterature study I have inferred that my ligand able to interact with my model only at open conformation. Now my questions are, 1) wheather can I proceed to docking with this model(modelled for closed conformation) to test the ligand interaction with the model? 2)Does docking softwares populary used, such as one I am having the Autodock will take care of this drawback? Kidly help me, B.Natara, M.Tech.,(Bioinformatics), SASTRA Deemed University, Thanjavur, Tamil Nadu, India. --------------------------------- Yahoo! Messenger - Communicate instantly..."Ping" your friends today! Download Messenger Now

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Re: modeller_usage Digest, Vol 3, Issue 36
by Azat Badretdinov 31 Mar '04

31 Mar '04

> Message: 4 > Date: Tue, 30 Mar 2004 16:55:59 -0500 > From: "Clemens Steegborn" <cls2001(a)med.cornell.edu> > Subject: [modeller_usage] problem reading alignment file > To: modeller_usage(a)salilab.org > Message-ID: <5.2.0.9.2.20040330164627.00b485d0(a)pop.med.cornell.edu> > Content-Type: text/plain; charset="us-ascii"; format=flowed > > > Hi, > > I'm using the WINDOWS version of MODELLER6v2 > > I get the following error when reading the template and alignment files: > > > > >TOP_________> 121 107 CHECK_ALIGNMENT > > > >check_a_343_> >> BEGINNING OF COMMAND > >openf5__224_> Open 11 OLD SEQUENTIAL myt.atm > >rdabrk__290E> Number of residues in the alignment and pdb files are > different: 433 392 > > For alignment entry: 1 > >recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > the problem seems to be that MODELLER doesn't understand the gap residue > '-', as it also > doesn't understand '/' (using '/' gives an error stating it doesn't know > this residue)! > > I tried including a link called RESTYP_LIB to restyp.lib in the libs.lib > file, but that didn't help. > > Any suggestions would be appreciated! > Hi, Clemens, Weird. It is not clear why would you have to modify your libs.lib file, since normally it contains the setting for RESTYP_LIB? Do you have your own customized restyp.lib at a different location? I assume your *LIB settings in libs.lib are more or less similar (like in the default setting). If that is the case and if RESTYP_LIB setting would be incorrect, then other library settings would cause problems as well. I wonder if you can send your input files (.pdb, .ali, libs.lib and restyp.lib). Azat A.Ya.Badretdinov, PhD, Sr. Scientist x5728 http://intranet.accelrys.com/~azat > Clemens > > > > ------------------------------ > > _______________________________________________ > modeller_usage mailing list > modeller_usage(a)salilab.org > http://salilab.org/mailman/listinfo/modeller_usage > > > End of modeller_usage Digest, Vol 3, Issue 36 > *********************************************

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Re: [modeller_usage] problem reading alignment file
by Eric Feyfant 31 Mar '04

31 Mar '04

Hi Clemens; I suggest you to extract the sequence using modeller : basically: Read the pdb file set ADD_SEQUENCE on and write the alignment. And you will see what sequence modeller consider. As far as I know Modeller never had issues with gap and "/" which correspond to a TER in your pdb file. Eric >>> "Clemens Steegborn" <cls2001(a)med.cornell.edu> 3/30/2004 4:55:59 PM >>> Hi, I'm using the WINDOWS version of MODELLER6v2 I get the following error when reading the template and alignment files: > >TOP_________> 121 107 CHECK_ALIGNMENT > >check_a_343_> >> BEGINNING OF COMMAND >openf5__224_> Open 11 OLD SEQUENTIAL myt.atm >rdabrk__290E> Number of residues in the alignment and pdb files are different: 433 392 > For alignment entry: 1 >recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > the problem seems to be that MODELLER doesn't understand the gap residue '-', as it also doesn't understand '/' (using '/' gives an error stating it doesn't know this residue)! I tried including a link called RESTYP_LIB to restyp.lib in the libs.lib file, but that didn't help. Any suggestions would be appreciated! Clemens _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org http://salilab.org/mailman/listinfo/modeller_usage

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RE: [modeller_usage] problem reading alignment file
by Schweikardt, Thorsten 31 Mar '04

31 Mar '04

Hi Clemens, the error you describe usually appears when your pdb- file has some missing aminoacids in respect to the sequence you use in the alignment-file. Modeller states that your pdb contains 392 residues, but your alignment contains 433. You can use DeepView to open your template and save its aminoacid-sequence (File-Save-Save Sequence as FASTA). Compare it to the sequence in your alignment file, they should be identical. If not, correct the align- ment. Hope this helps. Concerning the '/' and '-', I have no problems using them on the linux-version. Best wishes, Thorsten Schweikardt Molecular Biophysics University Mainz, Germany > I'm using the WINDOWS version of MODELLER6v2 > > I get the following error when reading the template and > alignment files: > >openf5__224_> Open 11 OLD SEQUENTIAL myt.atm > >rdabrk__290E> Number of residues in the alignment and pdb > files are > different: 433 392 > > For alignment entry: 1 > >recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > the problem seems to be that MODELLER doesn't understand the > gap residue '-', as it also doesn't understand '/' (using '/' > gives an error stating it doesn't know this residue)! >

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Count problem
by hemant kushwaha 30 Mar '04

30 Mar '04

Dear sir, I am facing a problem in getting my model of an allosteric enzyme and the prblem is with the count in the pdbfile and the alignment file the top file i am using 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 = 'template.ali' # alignment filename SET KNOWNS = '1BDG' '1DGK' '1CZA' 1BG3' '1HKC' ' # codes of the templates SET SEQUENCE = '1Str' # code of the target SET ATOM_FILES_DIRECTORY = '/disk1/project/ratnesh/pdbfiles' # 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) SET HETATM_IO = on # include heteroatom in the model #SET WATER_IO = on CALL ROUTINE = 'model' # do homology modelling and the error i am getting in logfile is as follows: Read the alignment from file : templatefile.ali Total number of alignment positions: 953 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1HKB 905 3 1HKB undefined 2 1DGK 903 3 1DGK undefined 3 1CZA 903 3 1CZA undefined 4 1BG3 893 3 1BG3 undefined 5 1HKC 901 3 1HKC undefined 6 1Str 493 1 1Str Candida albicans TOP_________> 122 107 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1HKB.pdb openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1DGK.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 2 902 33 GLYP 113 ADP RTppp## rdabrk__288W> Protein not accepted: 2 openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1CZA.pdb rdabrk__291E> Sequence difference between alignment and pdb : STRUCTURE RES_IND ALN_ITYP ALN_RES X_ITYP X_RES -----*----- 3 903 33 GLYP 113 ADP Tpppp# rdabrk__288W> Protein not accepted: 3 openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1BG3.pdb openf5__224_> Open 11 OLD SEQUENTIAL /disk1/project/ratnesh/pdbfiles/1HKC.pdb fndatmi_285W> Number of residues <> number of atoms; atom code: 905 901 CA check_a_337E> Structure not read in: 2 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 20689357 20204.449 19.731 Starting time : 2004/03/29 17:26:50.612 Closing time : 2004/03/29 17:27:04.831 Total CPU time [seconds] : 0.00 Can u help in sorting out what is this error and how it can be solved warm regards hemant __________________________________ Do you Yahoo!? Yahoo! Finance Tax Center - File online. File on time. http://taxes.yahoo.com/filing.html

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