- modeller_usage - salilab.org

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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clustering problem
by Xin Hu 03 Feb '05

03 Feb '05

Dear Modeller, I try to do a loop modeling using the following script. I got the xxx.BL####0000.pdb and DL#### output files, but the job stop at the step for clustering, the error showed like that: TOP_________> 1512 686 END_DO TOP_________> 1513 687 RETURN TOP_________> 1514 748 CALL ROUTINE = 'cluster', ID1 = 1, ID2 = 20 TOP_________> 1515 606 IF ARGUMENTS CLUSTER_CUT 0, OPERATION = 'LT', THEN = 'SET; CLUSTER_CUT = 1.5' TOP_________> 1516 607 READ_MODEL FILE = MODEL, ALIGN_CODES = ROOT_NAME pdbnam__217W> Filename for PDB code not found: undefined Directories: ./:../atom_files Extensions : :.atm:.pdb:.ent:.crd openf5__224_> Open 11 OLD SEQUENTIAL file-not-found openf5__225E> File does not exist: file-not-found openf5__224_> Open 11 OLD SEQUENTIAL file-not-found openf5__225E> File does not exist: file-not-found rdatm___297_> Segments, residues, atoms: 1 319 2467 rdatm___298_> Segment: 1 C 2467 iatmcls_286W> MODEL atom not classified: UNK: UNK iatmcls_286W> MODEL atom not classified: UNK: UNK iatmcls_286W> MODEL atom not classified: UNK: UNK iatmcls_286W> MODEL atom not classified: UNK: UNK iatmcls_286W> MODEL atom not classified: UNK: UNK ................... Dynamically allocated memory at amaxseq [B,kB,MB]: 22095569 21577.703 21.072 pdbnam__217W> Filename for PDB code not found: YpkA.BL99990001.pdb Directories: ./:../atom_files Extensions : :.atm:.pdb:.ent:.crd rdabrk__288W> Protein not accepted: 1 pdbnam__217W> Filename for PDB code not found: YpkA.BL99990002.pdb Directories: ./:../atom_files Extensions : :.atm:.pdb:.ent:.crd ............... fndatmi_285W> Number of residues <> number of atoms; atom code: 319 168 CA fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Could you please help me figure out the problem? Thank you very much! Xin Here is the top file: =============== INCLUDE #DEFINE_STRING VARIABLES = LOOP_CSRFILE LOOP_INI_MODEL SET OUTPUT_CONTROL = 1 1 1 1 1 SET SEQUENCE = 'YpkA' SET LOOP_MODEL = 'YpkA_modelB.pdb' SET ATOM_FILES_DIRECTORY = './:../atom_files' SET PDB_EXT = '.pdb' SET LOOP_STARTING_MODEL = 1 SET LOOP_ENDING_MODEL = 20 SET LOOP_MD_LEVEL = 'refine_3' SET RAND_SEED = -21840 CALL ROUTINE = 'loop' CALL ROUTINE = 'cluster', ID1 = 1, ID2 = 20 SUBROUTINE ROUTINE = 'select_loop_atoms' PICK_ATOMS SELECTION_SEGMENT = '203:' '256:', SELECTION_STATUS = 'initialize' RETURN END_SUBROUTINE ============== --

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[modeller_usage] Re: Inclusion of zinc atoms, Add_restraint problem?
by Cardenas, Alfredo 02 Feb '05

02 Feb '05

Hi again, I have tried to solve the problem that I described last Friday but without success. I was looking more carefully the log file (that was submitted in my first post) and there is something really strange. Maybe some of the more expert users could help me with this. When the program starts to run it generate a file pkci (that is the name of my sequence) that contains coordinates for the model. I assume this is the ini file (I am not sure why the ini extension is omitted). The number of atoms in this file is 890 (including 2 Zn atoms). I used this file to extract the ID for the residues coordinated with the Zn, information that is input in the ali file. The special restraints are read correctly as is evident from the log file: Dynamically allocated memory at amaxseq [B,kB,MB]: 5097041 4977.579 4.861 TOP_________> 216 163 CALL ROUTINE = 'special_restraints' TOP_________> 217 756 ADD_RESTRAINT ATOM_IDS = 'SG:14' 'ZN:55', RESTRAINT_PARAM; ETERS = 2 1 1 22 2 2 0 3.5 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 218 757 ADD_RESTRAINT ATOM_IDS = 'SG:17' 'ZN:55', RESTRAINT_PARAM; ETERS = 2 1 1 22 2 2 0 3.5 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 219 758 ADD_RESTRAINT ATOM_IDS = 'NE2:39' 'ZN:55', RESTRAINT_PARA; METERS = 2 1 1 22 2 2 0 3.5 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 220 759 ADD_RESTRAINT ATOM_IDS = 'SG:42' 'ZN:55', RESTRAINT_PARAM; ETERS = 2 1 1 22 2 2 0 3.5 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 221 760 ADD_RESTRAINT ATOM_IDS = 'SG:31' 'ZN:54', RESTRAINT_PARAM; ETERS = 2 1 1 22 2 2 0 3.5 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 222 761 ADD_RESTRAINT ATOM_IDS = 'SG:34' 'ZN:54', RESTRAINT_PARAM; ETERS = 2 1 1 22 2 2 0 3.5 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 223 762 ADD_RESTRAINT ATOM_IDS = 'SG:50' 'ZN:54', RESTRAINT_PARAM; ETERS = 2 1 1 22 2 2 0 3.5 0.1 Dynamically allocated memory at amprmcns [B,kB,MB]: 5097191 4977.726 4.861 TOP_________> 224 763 ADD_RESTRAINT ATOM_IDS = 'NE2:53' 'ZN:54', RESTRAINT_PARA; METERS = 2 1 1 22 2 2 0 3.5 0.1 After that the model file is read again: openf5__224_> Open 18 UNKNOWN SEQUENTIAL pkci.D00000001 TOP_________> 243 218 READ_MODEL FILE = MODEL openf5__224_> Open 11 OLD SEQUENTIAL pkci.ini openf5__224_> Open 11 OLD SEQUENTIAL pkci.ini rdatm___297_> Segments, residues, atoms: 2 55 438 rdatm___298_> Segment: 1 1 53 436 rdatm___298_> Segment: 2 54 55 2 TOP_________> 244 219 CALL ROUTINE = 'select_atoms' But the strange thing is that the number of atoms in the file is 438 not 890 as in the pkci file generated initially So after a few lines the log file gives an out of bounds message: csrrng__299E> Atom index is out of bounds: 441 438 Any ideas of what is going on here? By the way, I am running in windows. Thanks Alfredo Cardenas

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SO4 ion coordinates not written
by Cheri M Turman 02 Feb '05

02 Feb '05

I did have both: SET HETATM_IO = on, WATER_IO = on However, the water coordinates were generated and also my heme hetatm had generated coordinates. The SO4s were the only ones that didn't work. This is why I am thinking it has something to do with the settings in restyp.lib. Any other ideas? Cheri > Hi fellow modellers, > I am trying to model my protein with SO4 included in the template pdb > file. My problem first started when I used # for sulfate ion in my .ali > file but MODELLER stopped early with an error where it was trying to > match up the SO4 with GLYP. I thought this was probably because # is > used for GLYP in the restyp.lib file and it is the first one defined in > the list with a #. Therefore, I changed # to s for SO4 (also changed > the original s for sarcosine to #). The model was produced but no > coordinates were written for sulfate ions. Does anyone know what I > might need to do to get the coordinates written? Cheri SET HETATM_IO=on This allows the 'HETATM' groups to be written to the model file. j. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 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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SO4 ion coordinates not written
by Cheri M Turman 01 Feb '05

01 Feb '05

Hi fellow modellers, I am trying to model my protein with SO4 included in the template pdb file. My problem first started when I used # for sulfate ion in my .ali file but MODELLER stopped early with an error where it was trying to match up the SO4 with GLYP. I thought this was probably because # is used for GLYP in the restyp.lib file and it is the first one defined in the list with a #. Therefore, I changed # to s for SO4 (also changed the original s for sarcosine to #). The model was produced but no coordinates were written for sulfate ions. Does anyone know what I might need to do to get the coordinates written? 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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problem!
by vivek sharma 01 Feb '05

01 Feb '05

Dear Ben, Just let me know if there is anything wrong in this method. I am generating 50 structures for a template and as I told you program crashed with 'Internal Error' message as 'Energy (= NaN)' value gone out of the limits after generating 29 models. As you said to refine the structure before modelling, but I couldn't find a direct method to do that in inbuilt 'model' script, instead, I am generating 10 structures at a time with different RAND_SEED value in each run, therefore running this 5 times (different RAND_SEED values) to get again 50 structures. Is this OK? Yes, program runs fine. Please let me know, if there is any flaw in this procedure as compared to a single run of generation of 50 structures. I will be thankful. thanks and regards, Vivek Sharma --------------------old message--------------- Date: Fri, 28 Jan 2005 19:12:59 +0200 From: vivek sharma <vivek.sharma(a)helsinki.fi> Reply-To: vivek sharma <vivek.sharma(a)helsinki.fi> Subject: problem To: modeller_usage(a)salilab.org Dear Sir, I am a regular user of MODELER and I use 6v2. But now when I was generating 50 structures of a target using some templates, program ran fine till generating first 28 structures but died in 29 structure generation with the error mentioned below (please see below). For, the first time I have observed this error. What can be the problem. In the last statements of optimization schedule in log file you can see the current value of energy is mentioned by 'NaN'. What does this mean, looks like 'energy' has gone out of certain limits. 31 Non-bonded restraints : 1.0000 32 Atomic accessibility restraints : 1.0000 33 Atomic density restraints : 1.0000 Initial value of energy before optimization : 35818.9410 Current energy : NaN Symmetry term within energy : 0.0000 Optimizer exit status : 1 Number of iterations : 1 Number of calls to energy function : 201 Number of updates of dynamic contacts : 1 Number of non-updates of dynamic contacts : 201 Final maximal atomic shift : 0.000 TOP_________> 7609 235 IF ARGUMENTS = WRITE_INTERMEDIATES 1, OPERATION = 'EQ', ; THEN = 'WRITE_MODEL FILE = default, FILE_EXT = P; DB_EXT, FILE_ID = .B' TOP_________> 7610 236 IF ARGUMENTS = ERROR_STATUS 0, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 7611 237 IF ARGUMENTS = MOLPDF MAX_MOLPDF, OPERATION = 'GT', ; THEN = 'GO_TO __ABORT' TOP_________> 7612 238 END_DO TOP_________> 7613 232 OPERATE ARGUMENTS = ID1 1, OPERATION = 'SUM', RESULT = ID; 1 TOP_________> 7614 233 PICK_RESTRAINTS ADD_RESTRAINTS = OFF pick_re_612_> Number of MODEL atoms, selected restraints; 3854 49753 TOP_________> 7615 234 OPTIMIZE getcell_247E> Internal error: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 55660213 54355.680 53.082 Starting time : 2005/01/28 14:43:47.350 Closing time : 2005/01/28 18:09:34.578 Total CPU time [seconds] : 12315.51 Please have a look to the error, and suggest what can be the reason. I am first time facing such strange error, otherwise MODELER has worked fine always. Regards, Vivek -- VIVEK SHARMA "You must be the change you wish to see in the world." MKG ----- End forwarded message ----- -- VIVEK SHARMA HBG BI "You must be the change you wish to see in the world." MKG

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modelling heterodimer.
by DUVVURU Raja 01 Feb '05

01 Feb '05

Dear all, I am new to such a wonderfull software. i have a question regarding the modeller usage. i want to modell a heterotetramer i.e protein complex formed by two homodimeric proteins. is there any way that i could do it using the modeller. if this is not possible please let me know if there is a way to model homodimers or heterodimers using modeller. thanking you.

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