- modeller_usage - salilab.org

how to predict the model as a dimer
by Tong Chen 17 Feb '05

17 Feb '05

Hi! All: My template protein is a dimer, and the target protein is suppose to be a dimer as well. How can I get the dimer model in Modeller? Thanks a lot Tong Tong Chen School of Biological Sciences Flinders University GPO Box 2100 Adelaide 5001 Email: Tong.Chen(a)flinders.edu.au Phone: (08) 8201-3836

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redundant error check_a_337E> Structure not read in: 1
by Nicolas 16 Feb '05

16 Feb '05

Hello, I havealigned two sequences and want to modelise one of them. I applied to my file all the previous suggestions evoqued in the archive (SET OUTPUT_CONTROL = 1 1 1 1 1, corrected the format of my PIR alignement). Yet I still get the same error message. When I try to check my alignement, i also get this message. Does any body have any idea? here is the output TOP_________> 109 749 SET ALNFILE = 'ali.pir' TOP_________> 110 750 SET KNOWNS = '1ayx' TOP_________> 111 751 SET SEQUENCE = 'KPB1' TOP_________> 112 752 SET STARTING_MODEL = 1 TOP_________> 113 753 SET ENDING_MODEL = 5 TOP_________> 114 754 CALL ROUTINE = 'model' TOP_________> 115 419 CALL ROUTINE = 'getnames' TOP_________> 116 534 STRING_IF STRING_ARGUMENTS = MODEL 'undefined', OPERATION; = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATENA; TE, STRING_ARGUMENTS = SEQUENCE .ini, RESULT = MODEL' TOP_________> 117 535 STRING_IF STRING_ARGUMENTS = CSRFILE 'undefined', OPERATI; ON = 'EQ', THEN = 'STRING_OPERATE OPERATION = CONCATE; NATE, STRING_ARGUMENTS = SEQUENCE .rsr, RESULT = CSRFILE; ' TOP_________> 118 536 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.sch', RESULT = SCHFILE TOP_________> 119 537 STRING_OPERATE OPERATION = 'CONCATENATE', ; STRING_ARGUMENTS = SEQUENCE '.mat', RESULT = MATRIX_FI; LE TOP_________> 120 538 SET ROOT_NAME = SEQUENCE TOP_________> 121 539 RETURN TOP_________> 122 420 CALL ROUTINE = 'homcsr' TOP_________> 123 112 READ_ALIGNMENT FILE = ALNFILE, ALIGN_CODES = KNOWNS SEQUE; NCE Dynamically allocated memory at amaxseq [B,kB,MB]: 84067 82.097 0.080 openf5__224_> Open 20 OLD SEQUENTIAL ali.pir Dynamically allocated memory at amaxbnd [B,kB,MB]: 8049459 7860.800 7.677 openf5__224_> Open 20 OLD SEQUENTIAL ali.pir Read the alignment from file : ali.pir Total number of alignment positions: 500 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1ayx 446 1 glucoamlyse 2 KPB1 394 1 alpha subun TOP_________> 124 113 STRING_IF STRING_ARGUMENTS = TOP_VERSION 'accelrys', OPER; ATION = 'ne', THEN = 'GO_TO __ACCELRYS1' TOP_________> 125 117 CHECK_ALIGNMENT check_a_343_> >> BEGINNING OF COMMAND check_a_337E> Structure not read in: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

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Modeller Help: New User
by Chaminda Basnayake 10 Feb '05

10 Feb '05

Dear Modeller Users, I am a new user to Modeller 7v7 and I am trying to model a protein with over 990 residues. I started in a Windows PC and all tutorial examples were processed without a problem. However, when I replaced the structure and the sequence from my protein, Modeller crashed with a stack overflow error. I got the following error message. forrtl: severe (170): Program Exception - stack overflow Image PC Routine Line Source mod7v7.exe 00507271 Unknown Unknown Unknown mod7v7.exe 004FEA3E Unknown Unknown Unknown mod7v7.exe 004589DE Unknown Unknown Unknown mod7v7.exe 0040653E Unknown Unknown Unknown mod7v7.exe 0040F5BB Unknown Unknown Unknown mod7v7.exe 006A564B Unknown Unknown Unknown mod7v7.exe 006EDB39 Unknown Unknown Unknown mod7v7.exe 006DC824 Unknown Unknown Unknown kernel32.dll 7C816D4F Unknown Unknown Unknown Then I tried with the modified version of Modeller (Updated Binary Version), only to find the same stack overflow error. So my first question is, is there a way to get around this and still do my analysis in a Windows PC? As a second attempt, I tried the same set of TOP files in a Linux environment. Unfortunately, I couldn't get to work even the simplest TOP scripts in Linux environment. For instance, the following script and log shows a set that runs fine in the Windows environment but not in the Linux. I assume that this is a result of a simple mistake. How do I fix this? Can someone suggest a way to get this done either in Windows or in Linux? Thank you! Cham TOP script: INCLUDE SET ALNFILE = 'TvLDH-4mdhA.ali' SET KNOWNS = '4mdh' SET SEQUENCE = 'TvLDH' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 CALL ROUTINE = 'model' LOG file: assgn___544E> Variable name not recognized: ALNFILE Command line: SET ALNFILE = 'TvLDH-4mdhA.ali' assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: KNOWNS Command line: SET KNOWNS = '4mdh' assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: STARTING_MODEL Command line: SET STARTING_MODEL = 1 assgn___525E> Error in TOP variable assignment. assgn___544E> Variable name not recognized: ENDING_MODEL Command line: SET ENDING_MODEL = 5 assgn___525E> Error in TOP variable assignment. compile_563E> Please correct the errors reported above and rerun MODELLER. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 56755 55.425 0.054 Starting time : 2005/02/10 09:17:56.036 Closing time : 2005/02/10 09:17:58.468 Total CPU time [seconds] : 2.37 ALI file: >P1;4mdh structureX:4mdh: 1 :A: 333 :A:undefined:undefined:-1.00:-1.00 SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEEI AFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKEN FSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQAKEVGVYEAVKDDSWLKGEFITT VQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIISDGNSYGVPDDLLYSFPVTIKDKTWKIVE GLPINDFSREKMDLTAKELAEEKETAFEFLSSA* >P1;TvLDH sequence:TvLDH: : : : ::: 0.00: 0.00 SEPIRVLVTGAAGQIAYSLLYSIGNGSVFGKDQPIILVLLDITPMMGVLDGVLMELQDCALPLLKDVIATDKEEI AFKDLDVAILVGSMPRRDGMERKDLLKANVKIFKCQGAALDKYAKKSVKVIVVGNPANTNCLTASKSAPSIPKEN FSCLTRLDHNRAKAQIALKLGVTSDDVKNVIIWGNHSSTQYPDVNHAKVKLQAKEVGVYEAVKDDSWLKGEFITT VQQRGAAVIKARKLSSAMSAAKAICDHVRDIWFGTPEGEFVSMGIISDGNSYGVPDDLLYSFPVTIKDKTWKIVE GLPINDFSREKMDLTAKELAEEKETAFEFLSSA*

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Re: problems defining a new residue type (continued)
by barmalay alterman 08 Feb '05

08 Feb '05

Hi again, I have changed the order of the entries in the radii.lib and radii14.lib files, so that the newly defined atoms are at the beginning. Now I am getting a new error message: read_to_240E> Include residue type in RESTYP_LIB: AAA recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I am a little surprised that the order of entries in the radii libraries matters (the comments there state otherwise). But in any event I would appreciate your help. __________________________________ Do you Yahoo!? Yahoo! Mail - You care about security. So do we. http://promotions.yahoo.com/new_mail

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problems defining a new residue type
by barmalay alterman 07 Feb '05

07 Feb '05

Hi, I've been trying to define a new residue type following stages a-d in section 17 of the FAQ chapter. I have updated the folowing *.lib files: top,models,restyp,par,radii,radii14. Then, as a first test I have used align2d.top to align a pdb file that contains this new residue with an identical sequence, but with the residue replaced by a standard one. Modeller did not recognize the new residue and it denoted it as X in the pap file. I got the following warnings: mkapsa__293W> No TOPOLOGY_LIB is in memory. Use READ_TOPOLOGY to read one. iup2crm_280W> No TOPOLOGY_LIB in memory or assigning a BLK residue. Default CHARMM atom type assigned: N --> N This message is written only for the first such atom. When I included the following two lines at the beginning of the align2d.top file: READ_RESTYP_LIB RESTYP_LIB_FILE= '$(LIB)/restyp.lib' READ_TOPOLOGY FILE = '$(LIB)/top.lib', ADD_TOPOLOGY = on I got the following error message: read_to_231E> CHARMM atom type is not recognized (not in RADII_LIB): CR15 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 (I got the same when the ADD_TOPOLOGY was off). But the radii.lib file definitely contains the relevant atoms. I'm puzzled. Any suggestions? Thanks a lot, O __________________________________ Do you Yahoo!? Yahoo! Mail - Find what you need with new enhanced search. http://info.mail.yahoo.com/mail_250

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another stack overflow
by DUVVURU Raja 05 Feb '05

05 Feb '05

Hellow everybody, here is another type of stack overflow problem.i am sure that it is different than from the previous one. on my computer when i first installed the modeller7v7 and run it i got the same stack overflow problem as discussed previously in our mail group. and then i could rectify that as suggested by the experts.it is working fine when i used "full_homol" routein. however when i try to use the "full_homol" routein coupled with the Heteroatoms (copper; NAG;o), water etc inculded i get the stack overflow problem after couple of minuts and the message displayed below is shoen on screen ====================================================================== on screen errpr msg ====================================================================== C:\Program Files\Modeller7v7\examples\tutorial-model\fox1>fox1_cu.top forrtl: severe (170): Program Exception - stack overflow Image PC Routine Line Source mod7v7.exe 00507271 Unknown Unknown Unknown mod7v7.exe 004FEA3E Unknown Unknown Unknown mod7v7.exe 004589DE Unknown Unknown Unknown mod7v7.exe 0040653E Unknown Unknown Unknown mod7v7.exe 0040F5BB Unknown Unknown Unknown mod7v7.exe 006A564B Unknown Unknown Unknown mod7v7.exe 006EDB39 Unknown Unknown Unknown mod7v7.exe 006DC824 Unknown Unknown Unknown kernel32.dll 7C816D4F Unknown Unknown Unknown C:\Program Files\Modeller7v7\examples\tutorial-model\fox1> ======================================================================= *********************************************************************** My top file: ( isuspect this file) *********************************************************************** # A sample TOP file for fully automated comparative modeling INCLUDE # include MODELLER routines SET ATOM_FILES_DIRECTORY = './:../fox1' # directory with input atom files SET SEGFILE = 'fox1.seg' # input file w/ templates and target SET KNOWNS = '1KCW' # templates' PDB codes SET SEQUENCE = 'fox1' # target code SET OUTPUT_CONTROL = 1 1 1 1 2 SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 SET TOPOLOGY_MODEL = 1, HYDROGEN_IO = ON, HETATM_IO = on, WATER_IO = ON SET TOPLIB = '$(LIB)/top.lib' SET PARLIB = '$(LIB)/par.lib' CALL ROUTINE = 'full_homol' # get alignment and a model ************************************************************************* can any one please help me with the problem. am i correct in making my top file. log file does not show any error messages. thanking you. yours truely. raja

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Re: SO4 ion coordinates not written
by Cheri M Turman 04 Feb '05

04 Feb '05

Me again, Modeling SO4 explicitly may be more complicated than I thought...not sure? However, I looked into what I guess are the CHARMM topology (top_all22_prot_b5.inp) and parameter (par_all22_prot_b5.inp) files that MODELLER uses by default and there was no entry for SO4. This is puzzling since SO4 is defined in the retyp.lib file. Has anyone been successful with changing SO4 single letter PDB entry in the restyp.lib and having MODELLER use top and parms for it? If so, where are the top and parms for SO4 located? Maybe I just overlooked them?? Anyway, I was able to get the SO4s to work using 'BLK' notation with '.' in the .ali file. If I read correctly, this means that there is no topology or parameters associated with 'BLK' so they are modeled as rigid bodies based on the template structure coordinates. They appear fine in the output coordinates so I am happy to proceed with this process. But, I would still like to know if there are CHARMM top and parms for SO4 if anyone knows. Cheers, Cheri ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Cheri M. Turman Graduate Student University of Texas-Houston Medical School 6431 Fannin Houston, TX 77030 USA e-mail: cheri.m.turman(a)uth.tmc.edu Ph.: 713-500-6126 Fax: 713-500-0652

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a question about SEQUENCE_SEARCH
by yunierkis＠uclv.edu.cu 04 Feb '05

04 Feb '05

Hi everyone I'm currently beginning using MODELLER. I have tried to run the basic example of the tutorial. When I run the SEQUENCE_SEARCH command (using the same script provided in the tutorial) it begin running and writing to the log file, but in certain moment MODELLER stops writing to the log file and never stops running. Those are the last lines written by MODELLER in to my log file _aln.pos 210 220 230 240 250 260 270 TvLDH TQKVVDVLDHDYVFDTFFKKIGHRAWDILEHRGFTSAASPTKAAIQHMKAWLFGTAPGEVLSMGIPVP 9wgaA E---------------------------FCGGGCQSGACSTDKPCGK-------DAGGRVCTNNYCCS _consrvd * * * * * * * _aln.pos 280 290 300 310 320 330 TvLDH EGNPYGIK Can anybody help me? Thanks in advance Yunierkis

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Re: Inclusion of zinc atoms, Add_restraint problem?
by Cardenas, Alfredo 04 Feb '05

04 Feb '05

I solved the problem. This was the original top file: INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignment1.txt' # alignment filename SET KNOWNS = '1PTQ' # codes of the templates SET SEQUENCE = 'pkci' # code of the target #SET TOPOLOGY_MODEL = 1 SET HETATM_IO = on SET TOPLIB = '$(LIB)/top.lib' SET PARLIB = '$(LIB)/par.lib' #SET ATOM_FILES_DIRECTORY = './:../atom_files' # 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 SUBROUTINE ROUTINE = 'special_restraints' ADD_RESTRAINT ATOM_IDS = 'SG:14' 'ZN:55', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'SG:17' 'ZN:55', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'NE2:39' 'ZN:55', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'SG:42' 'ZN:55', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'SG:31' 'ZN:54', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'SG:34' 'ZN:54', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'SG:50' 'ZN:54', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 ADD_RESTRAINT ATOM_IDS = 'NE2:53' 'ZN:54', ; RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 3.0 0.1 RETURN END_SUBROUTINE I was using top.lib (all hydrogen topology). When I changed it to top_heav things work. Alfredo Cardenas

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dymer modelling
by Edoardo Saccenti 04 Feb '05

04 Feb '05

Dear all I'm dealing with a little big problem. I need to model a dymer protein. I use as template the A and B chain of a PDB file containing A B C D chains. To create the sequence to be modelled I have pasted twice the monomer sequence. The program works fine but I get a model with only a chain double sized in respect of th original. In the original pdb A e B chains are not linked and I want a non linked dymer. Ho to do this? This the alignemet file I have used. >P1;1JU6 structureX:1JU6:28 :A:313:B :TYMS:Homo Sapiens:-1.00:-1.00 HGELQYLGQIQHILRCGVEKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEE LLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYR DMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSE LSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKI QLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPTIKMEMAVHGELQYLGQIQHIL RCGVEKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKEL SSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQL QRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGL GVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRI LRKVEKIDDFKAEDFQIEGYNPHPTIKMEMAV * >P1;TYMS_F117L_dym sequence:TYMS_F117L_dym: : : : :::-1.00:-1.00 HGELQYLGQIQHILRCGVEKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEE LLWFIKGSTNAKELSSKGVKIWDANGSRDLLDSLGFSTREEGDLGPVYGFQWRHFGAEYR DMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSE LSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKI QLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPTIKMEMAVHGELQYLGQIQHIL RCGVEKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKEL SSKGVKIWDANGSRDLLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQL QRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGL GVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRI LRKVEKIDDFKAEDFQIEGYNPHPTIKMEMAV * Dr. Edoardo Saccenti Fiorgen Foundation c\o CERM Magnetic Nuclear Resonance Research Center Scientific Pole - University of Florence via Luigi Sacconi 6, 50019 Sesto Fiorentino (FI) ITALY Tel: +39 055 4574193 Fax: +39 39 055 4574271 Mob: +39 333 2289912 saccenti(a)cerm.unifi.it www.cerm.unifi.it

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