- modeller_usage - salilab.org

Question on an error message
by Cen Gao 22 Jan '05

22 Jan '05

Hi, I am new to modeller,Now I am just doing some simple test on a protein,but both the target and template has some atom file other than residue which i have to consider during the simulation.So i have to include the HETATM_IO = 'on' in simulation,my top file is as follow: INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'seq.ali' SET KNOWNS = '1U19' SET SEQUENCE = '1U20' SET TOPOLOGY_MODEL = 1, HETATM_IO = 'on', WATER_IO = 'on' SET TOPLIB = '$(LIB)/top.lib' SET PARLIB = '$(LIB)/par.lib' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' But it give me some error information rdabrk__290E> Number of residues in the alignment and pdb files are different: 696 697 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I don't why,because the alignment file and pdb file is exactly right(I simply generate the alignment file from the pdb file using modeller). And if I don't turn HETATM_IO = 'on' and simply using the code INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 SET ALNFILE = 'seq.ali' SET KNOWNS = '1U19' SET SEQUENCE = '1U20' SET STARTING_MODEL = 1 SET ENDING_MODEL = 1 CALL ROUTINE = 'model' It works very well and give me the right target file.I am really confused about that.Can anyone give me some suggestion about my code.And I also wanna to ask if i want to take the non-residue atoms into consideration during modeller,is my method right?Thank you for your suggestion.

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Modeller multiple alignment
by Andreas Kowarsch 21 Jan '05

21 Jan '05

Hello all, i also tried to run my skript to create a multiple alignment. top-file: READ_MODEL FILE = '1HYZ.pdb', MODEL_SEGMENT 'FIRST:A''LAST:A' SEQUENCE_TO_ALI ALIGN_CODES = '1HYZ' READ_MODEL FILE = '1BIS.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' SEQUENCE_TO_ALI ALIGN_CODES = '1BIS',ADD_SEQUENCE = on READ_MODEL FILE = '1BIU.pdb', MODEL_SEGMENT 'FIRST:B''LAST:B' SEQUENCE_TO_ALI ALIGN_CODES = '1BIU',ADD_SEQUENCE = on SET ATOM_FILES = '1HYZ' '1BIS' '1BIU' MALIGN3D SET ADD_SEQUENCE = on, ALIGN_BLOCK = NUMB_OF_SEQUENCES READ_ALIGNMENT FILE = 'target.ali', ALIGN_CODES = ALIGN_CODES 'target', ADD_SEQUENCE = on ALIGN2D WRITE_ALIGNMENT FILE='target.ali', ALIGNMENT_FORMAT = 'PIR' WRITE_ALIGNMENT FILE='target.pap', ALIGNMENT_FORMAT = 'PAP' But my job don't terminate.... it always made the same log file log-file: Job starting time (YY/MM/DD HH:MM:SS): 2005/01/13 14:15:56.678 rdactio_534E> Command not recognized: recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 56755 55.425 0.054 Starting time : 2005/01/14 14:15:56.678 Closing time : 2005/01/14 14:15:57.612 Total CPU time [seconds] : 0.90 Please can anybody help me....

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Modeller 7v7 Stack problems, tried EVERYTHING!!!!
by Tom Petty 21 Jan '05

21 Jan '05

I have a windows XP SP2 IBM laptop with plenty of memory (512MB RAM) and processing speed. When I try to model a protein domain of about 750 residues (with a multiple alignment of only two sequences, the target and the strucutre sequence), the program runs for about 20-30 seconds and then I get this error: C:\Program Files\Modeller7v7\examples\tutorial-model>mod7v7 Toms-Initial 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 I've done all that is in my power to bump the memory management on my laptop, changing the virtual memory and paging sizes (to max). Editing the CONFIG.NT to explicitly stating number of stacks and stack size, etc. Nothing works! It seems that my computer should be able to handle modeller, no? Would you have any suggestions as to what may be going on and how to handle this? Also, I worked through the tutorial and it runs fine with the example files. Thanks for your help, All the best Tom Petty ----------------------------------- Graduate Student Genomics and Computational Biology Biomedical Graduate Studies University of Pennsylvania

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question
by drugdesign 18 Jan '05

18 Jan '05

I want to make homology modelling of TM domains without loops in GPCR. But I get error during calculatioons. What wrong I have done? Respectively yours, Andrew I use such alignment: >P1;1L9H X-ray:1L9H:37 : :307 : :rhodopsin:Bos Taurus: : FSMLAAYMFLLIMLGFPINF/YILLNLAVADLFMVFGGFTTT/NLEGFFATLGGEIALWSLVVL/AIMGVAFTWVMALACAAPPLV/FVIYMFVVHFIIPLIVIFFC/VTRMVIIMVIAFLICWLPYAG/FMTIPAFFAKTSAVYNPVIYI* >P1;1fdx sequence:fzd1:324 : :623 : :Frizzled:Homo Sapiens: : GIWSVLCCASTLFTVLTYLV/IIFLSGCYTAVAVAYIAGFLL/TILFMMLYFFSMASSIWWVIL/YFHLAAWAVPAIKTITILALG/FVLAPLFVYLFIGTSFLLAGF/IGVFSVLYTVPATIVIACYFY/VFMIKYLMTLIVGITSGFWIW *

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RE: [modeller_usage] question
by Schweikardt, Thorsten 18 Jan '05

18 Jan '05

Hi Andrew, it's hard to say what goes wrong as your email does not contain the error message or your input files, but I would guess the line X-ray:1L9H:37 : :307 : :rhodopsin:Bos Taurus: : causes the problem, it should read like this: structureX:1L9H:37 : :307 : :rhodopsin:Bos Taurus: : You should consult the modeller manual about the correct input file formats, to make sure there is not anything else wrong with your alignment: http://salilab.org/modeller/manual/node64.html I hope that helps. Best wishes, Thorsten Schweikardt Molekulare Biophysik Universität Mainz

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Re: modeller_usage Digest, Vol 4, Issue 1
by rathan kar 13 Jan '05

13 Jan '05

hi all iam facing a problem and i dont know as to which software should i use: 1. i have a protein whose first 100 residues matches one domain and the rest 136 residues a second one. is it logical to join these two domains and construct a protein and say that this protein has dual function. 2. if yes, then how do the orgins of these two models coincide. as far as i know we should use a rotation matrix to align these two. but i need a readymade software which is user freindly so that this can do that work. are there any such softwares other than INSIGHTII. PLZ REPLY --------------------------------- Do you Yahoo!? The all-new My Yahoo! Get yours free!

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Superposition problem
by Shamshad Zarina 29 Dec '04

29 Dec '04

Dear Modeller Community, I am trying to superpose two models using superpose command. The command runs okay and it creates a .fit file. Although the fit file looks fine but it has an unusual line connecting the last and first residues of both models. Any ideas why this is happening? thanks, Shamshad __________________________________ Do you Yahoo!? Yahoo! Mail - Easier than ever with enhanced search. Learn more. http://info.mail.yahoo.com/mail_250

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Re: [modeller_usage] (no subject)
by Modeller Caretaker 28 Dec '04

28 Dec '04

Anagha Joshi wrote: > when I try to run the basic model tutorial at modeller site > I run align2d.top > I get warning > 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: C --> CT2 > This message is written only for the first such atom. > fndatmi_285W> Number of residues <> number of atoms; atom code: 668 > 66 > 6 CA > fndatmi_285W> Number of residues <> number of atoms; atom code: 668 > 66 > 6 CA > I > don,t > understand what this warning is. It is only a warning, and can be ignored in this case. If you are going to build a comparative model, then Modeller needs to know that a 'CT2' atom is a carbon, so that it can match it against similar carbon atoms in the templates, and use molecular mechanics parameters defined for a CT2 atom. It gets this information from the topology and parameter files. However, for the case of alignment, this is not needed. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage

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Problems with stereo-chemical fixing of Hydrogen atoms
by Ravi Rathore 28 Dec '04

28 Dec '04

Dear modellers, Q: Is it possible to built short-contact-free models (hydrogens included) with Modeller? I am building an all-atom model using following scripts, In modeller 7v7: SET TOPOLOGY_MODEL = 1, HYDROGEN_IO = on SET TOPLIB = $(LIB)/top_allh.lib SET PARLIB = $(LIB)/par.lib CALL ROUTINE = 'model' ----------------------------------------- In modeller6: SET TOPOLOGY_MODEL = 1, HYDROGEN_IO = on SET TOPLIB = $(LIB)/top.lib (also tried top_allh.lib) SET PARLIB = $(LIB)/par.lib CALL ROUTINE = 'model' ------------------------------------------- The models do have hydrogen atoms, however, I noticed that most of the hydrogens have short-contacts within the same atom or residue OR with neighboring residues and also have long-range clashes. Assuming that there is everything fine with topology or parameter files, I wonder, the energy minimization/MD should have corrected such clashes. Then, I tried to use other, thorough optimization protocols, but of no use: SET LIBRARY_SCHEDULE = 1 SET MAX_VAR_ITERATIONS = 300 SET MD_LEVEL = 'refine_5' SET REPEAT_OPTIMIZATION = 3 SET MAX_MOLPDF = 1E6 I would be grateful for any suggestion on proper stereo-chemical fixing of hydrogen atoms with Modeller. Sincerely, Rathore, R.S. --------------------------------- Do you Yahoo!? Send holiday email and support a worthy cause. Do good.

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(no subject)
by anagha＠mbu.iisc.ernet.in 28 Dec '04

28 Dec '04

dear sir, I am new to modeller user and also to linux system. i have downloaded and installed modeller But as it doent have GUI. How will I start using it. I need help. Thank you Anagha

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