- modeller_usage - salilab.org

RE: [modeller_usage] Some Doubts
by Schweikardt, Thorsten 28 Jul '04

28 Jul '04

Hello Elton, your alignment file states "structure" where it should be "structureX", change it and Modeller should read in the pdb file, as long as you have stored it in the path you gave Modeller in the "SET ATOM_FILES_DIRECTORY"-command. You should also give Modeller the starting/ending aminoacid number and chain number in the alignment file. The second line should be structureX:1uw3:125:A:230:A:::-1.00:-1.00 Another thing: as long as you do not want to model water or ions, just protein, you should delete all but the aminoacid atoms from the input pdb-file, as modeller will try to match the residues in the alignment file with the pdb-file and will stop if it encounters atoms that are not present in both. For alignment file parameters, have a look at http://salilab.org/modeller/manual/node72.html I hope that helps, best wishes, Thorsten Schweikardt Molecular Biophysics University of Mainz > -----Original Message----- > From: modeller_usage-bounces(a)salilab.org > [mailto:modeller_usage-bounces@salilab.org] On Behalf Of > Elton Jose Rosas de Vasconcelos > Sent: Tuesday, July 27, 2004 11:43 PM > To: modeller_usage(a)salilab.org > Subject: [modeller_usage] Some Doubts > > Dear Doctors and Modeller users, > > We are graduate students in Fortaleza, Brazil and we are > trying to model > an aminoacid sequence deduced from genotyping data using the > MODELLER for > Linux (RedHat 9.0)! Thus, we would like to know if you could > help us on the > script for modelling our target sequence, cause we are having > some troubles > with that. Our log output file stops after the CHECK_ALIGNMENT, in the > BEGINNING OF COMMAND, telling us the template's structure had > not been read. > We put our atomic coordenates files (1uw3.atm and pdb1uw3.ent) into > the /examples/atom_files/ subdirectory. > > Another error message appears when we put, in alignment file > (pri.ali), > "structure" and "sequence" in front of the template and > target sequence > respectively. This error message is "rdpir___648E> Alignment > sequence not found > in PDB file: 1 ../atom_files/pdb1uw3.ent" > > Please check our *.top *.ali and *.log files attached. > > We would appreciate very much if you could give us some light > on solving this > problem. Beforehand I thank you for your attention... > > Vasconcelos, EJR and Nugen (Núcleo de Genômica e > Bioinformática) Group - > Fortaleza, Brazil >

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Dimer modelling with metals
by V Nadeem Ahmad 27 Jul '04

27 Jul '04

Dear Modellers, I would like to know how to do Dimer modelling in the vicinity of a metal ion present. else even modelling a protein chain i need to place a Metal ion in the protein how to go about it tell which script i can use and my alignment. with regards, Nadeem Ahmad V *************************************************************** V.Nadeem Ahmad B.Tech G-04,Techpark Mall Institute of Bioinformatics & Applied Biotechnology (IBAB) International Tech Park (ITPL) Whitefield, Banglore Phone: 080 -28410029 *************************************************************** "The harder you work, the luckier you get"

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Some Doubts
by Elton Jose Rosas de Vasconcelos 27 Jul '04

27 Jul '04

Dear Doctors and Modeller users, We are graduate students in Fortaleza, Brazil and we are trying to model an aminoacid sequence deduced from genotyping data using the MODELLER for Linux (RedHat 9.0)! Thus, we would like to know if you could help us on the script for modelling our target sequence, cause we are having some troubles with that. Our log output file stops after the CHECK_ALIGNMENT, in the BEGINNING OF COMMAND, telling us the template's structure had not been read. We put our atomic coordenates files (1uw3.atm and pdb1uw3.ent) into the /examples/atom_files/ subdirectory. Another error message appears when we put, in alignment file (pri.ali), "structure" and "sequence" in front of the template and target sequence respectively. This error message is "rdpir___648E> Alignment sequence not found in PDB file: 1 ../atom_files/pdb1uw3.ent" Please check our *.top *.ali and *.log files attached. We would appreciate very much if you could give us some light on solving this problem. Beforehand I thank you for your attention... Vasconcelos, EJR and Nugen (Núcleo de Genômica e Bioinformática) Group - Fortaleza, Brazil

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modeling mutations
by Miguel Relloso-Cereceda 26 Jul '04

26 Jul '04

Dear Modeler mailing list, I am a user of MODELLER 6v2 for Linux, and I am using this program to model the mutations that I am making on CD1b. I am looking for new interactions between amino acids that could be generated by these mutations and for possible changes generated in loops. This is the modeller that I am using: INCLUDE SET ATOM_FILES_DIRECTORY = '/home/moodyb/Miguel/37t/' SET OUTPUT_CONTROL = 1 1 1 1 1 #SET PDB_EXT = '.pdb' #SET MD_LEVEL = 'refine1' SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 #SET DEVIATION = 4.0 SET KNOWNS = 'CD1b' #SET HETATM_IO = off #SET WATER_IO = off #SET HYDROGEN_IO = off #SET ALIGNMENT_FORMAT = 'PIR' SET SEQUENCE = 'CD1b-37t' SET ALNFILE = '37t.pir' CALL ROUTINE = 'model' Are these parameters the best way to get my objectives? I do not have much experience in computer science, and I went through your manual and I did not understand it at all. Please contact me with any advice and if it is not convenient, could you tell me who might be able to help me? Thank you very much. Miguel Relloso. ----------------------oOO-(_)-OOo---------------- Miguel Relloso Ph.D. Brigham & Women's Hospital Harvard Medical School Smith 514 1 Jimmy Fund Way Boston, MA 02115 phone: 617.525.1027 fax: 617.525.1010

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Re: [modeller_usage] Restraints Problem
by akshay17 23 Jul '04

23 Jul '04

Dear Sir I tried rearranging parameters and Atom_ids which were written in wrong order in my .rsr file. This time, it says "segmentation fault (core dumped)". I recognize my problem somewhat similar to Mr. Daniele Bemporad's but as advised by you, i think in his .rsr file also, the parameters and Atom_ids are other way around. Anyway, i guess there might be some other problem apart from that. I am attaching my .rsr, .top & .log files. Is it possible that the User restraints i am giving might be unreasonable to be met during the model generation due to which it halts? I am not sure. Thanks for your help. Akshay Patny > > > On Tue, Jul 20, 2004 at 12:05:36AM -0500, akshay17 > > > wrote: Dear Sir, I tried removing Extra lines from my > > > .rsr file and still got the following error. > > > > > > > > > __________________________________________________________ > > > __ _ Executing Modeler Additional output in file > > > angim_06.log and in angim_06.log.moltabfile, > > > angim_06.log.restabfile, angim_06.log.viotabfile* > > > > > > lib-4190 : UNRECOVERABLE library error > > > A numeric input field contains an invalid character. > > > > > > Encountered during a list-directed READ from an > > > internal file (character variable) > > > IOT Trap > > > Abort (core dumped) > > > > > > > > > __________________________________________________________ > > __ _ > > > > Please advise. Shall, i write MODELLER 5 or MODELLER > > > 6v2 in my .rsr file. I am attaching my .rsr file > again. > > > The format of your restraints file is incorrect; see > > http://salilab.org/modeller/manual/node98.html. The > > first line must read either 'MODELLER5 VERSION: MODELLER > > FORMAT' or 'MODELLER5 VERSION: USER FORMAT'. There is no > > 'MODELLER6v2' format. Additionally, your user format > > lines are incorrect - the format should be: > > > > Id Form Modality Feature Group Numb_atoms > > Numb_parameters 0 Parameters Atom_ids > > > > - i.e., you have your parameters and Atom_ids the wrong > > way round. Your restraints file should look something > > like the following: > > > > MODELLER5 VERSION: USER FORMAT > > R 2 1 1 22 2 2 0 5.0 1.0 NZ:102 > > OD1:278 R 2 1 1 22 2 2 0 5.0 1.0 NZ:102 > > CZ:92 R 2 1 1 22 2 2 0 5.0 1.0 CZ:167 > > CG:263 R 2 1 1 22 2 2 0 5.0 1.0 NZ:199 > > CZ:259 R 2 1 1 22 2 2 0 5.0 1.0 OH:292 > > OD1:295 R 2 1 1 22 2 2 0 5.0 1.0 OH:292 > > OD1:111 R 2 1 1 22 2 2 0 5.0 1.0 NZ:240 > OD1:237 > > > Ben Webb, Modeller Caretaker > > -- > > modeller-care(a)salilab.org > > http://www.salilab.org/modeller/ Modeller mailing list: > > http://salilab.org/mailman/listinfo/modeller_usage > > > > Akshay Patny > (Graduate Student @ PhD) > Department of Medicinal Chemistry > School of Pharmacy, University of Mississippi > 417, Faser Hall, University, MS - 38677 > Tel : 662-915-1286(Off.), 662-236-3059(Res.) > E-mail : akshaypatny(a)indiatimes.com, akshay17(a)olemiss.edu > Web : www.olemiss.edu > > Akshay Patny (Graduate Student @ PhD) Department of Medicinal Chemistry School of Pharmacy, University of Mississippi 417, Faser Hall, University, MS - 38677 Tel : 662-915-1286(Off.), 662-236-3059(Res.) E-mail : akshaypatny(a)indiatimes.com, akshay17(a)olemiss.edu Web : www.olemiss.edu

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Installation prob on linux
by Joel Tyndall 22 Jul '04

22 Jul '04

Hi folks, I'm trying to install Modeller on my linux box and I get this error when I run tests. [jtyndall@allroy examples]# ./Run_tests DIR: ./wild_card ? FORTRAN Runtime Error: ? Bad file specification ? OPEN(UNIT=11,... ? FORTRAN Runtime Error: ? Bad file specification ? OPEN(UNIT=11,... DIR: ./all-steps ? FORTRAN Runtime Error: ? Bad file specification ? OPEN(UNIT=11,... ? FORTRAN Runtime Error: ? Bad file specification ? OPEN(UNIT=11,... ? FORTRAN Runtime Error: ? Bad file specification ? OPEN(UNIT=11,... ? FORTRAN Runtime Error: ? Bad file specification ? OPEN(UNIT=11,... ............etc I'm running fedora core 2 and I'm still a novice at this intsallation game. Any tips would be much appreciated. 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

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Array overflow error?
by Evans Adolfo Tapia 22 Jul '04

22 Jul '04

Hi, I'm using modeller lately, and I haven't had any problems while predicting the tertiary structure of a target using in the multiple alignment sequences with pdb files. Now that I'm trying to use, only CA files I receive this message and obviously Modeller stops the execution... > Array too small. Increase MPRMCNS > current maximum, current need: 1393200 1393224 Do you know if this is a parameter I can increase? or what can be causing the error. Let me explain a little, I'm obtaining these CA files using other methods to find the 3d structure of a given protein X. Then I get obtain all these files X1, X2, X3,... and make a multiple alignment using the same sequence of protein X as the target sequence and the sequences of each X1, X2, X3, that can differ from X in a few residues, as know structures. Then I'm trying to feed all these 3d models of the same protein and the alignment to modeller so I can obtain a refined 3D structure. But I get the above error, any help. Thanks, Evans

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error STDEV < 0 (no lig in second template)
by Jacques Zylberg 22 Jul '04

22 Jul '04

I have read and understood the problem and the answer. I have a similar problem : in one template there is a ligand and in the second there is no ligand, and thus i think this error is generated... (the relevant ligand is an ATP and MG which are present in one template and absent in the other). I use gaps to compensate the missing ligands and I still get the error messages Dynamically allocated memory at amprmcns [B,kB,MB]: 16912855 16516.461 16.129 make_re_417_> Restraint type to be calculated: distance r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 ..... r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 r_dista_644W> Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 stdevs__397E> STDEV < 0: -0.2287 Set to 1E-5. recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 16912855 16516.461 16.129 Starting time : 2004/07/22 14:48:09.689 Closing time : 2004/07/22 14:48:45.264 Total CPU time [seconds] : 0.00 This error message is usually encountered when two residues in the target sequence are aligned with two or more template distances that are very different, so that the corresponding combined restraint cannot be reproduced accurately by a cubic spline. Almost invariably, this error occurs when there is an error in the alignment (ie, one template 'says' a particular target distance should be close to 10A and the other template says it should be 20A). But in your case, it seems something else may be wrong, because stdev is less than 0. Would you please modify file $MODINSTALL6v2/modlib/messages.lib from M 644 3 1 Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 To (add @S1 in the fourth line, and keep a blank line after the @S1): M 644 3 1 Two basis restraints have means too far apart: ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 @S1 And email me the log file output. I know the message should be more informative and it should print what the violating distance is, and some day we will get there ;-) I hope this helps. Best, Andrej -- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali(a)salilab.org; Web http://salilab.org > -----Original Message----- > From: owner-modeller_usage(a)salilab.org > [">mailto:owner-modeller_usage@salilab.org] On Behalf Of Guittet, Muriel > Sent: Friday, March 21, 2003 12:32 PM > To: modeller_usage(a)salilab.org > Subject: error STDEV < 0: > > > Dear Modellers, > > I saw that someone already encoutered that error in the > modeller digest .. but unfortunately there was no answer (or > just to use the "output='long'" command what I did without > any answer) I try to model a protein structure, using 4 > different templates with about 30% of sequence identity with > the target. > > Modeller always send me the same error message: > r_dista_644W> Two basis restraints have means too far apart: > > ICSR MEAN1 MEAN2 STDEV1 STDEV2 R.VIOL1 R.VIOL2 NEW_SD1 NEW_SD2 > > stdevs__397E> STDEV < 0: -0.1509 > > Set to 1E-5. > > recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 > > > > Could someone explain me the meaning of this and how to fix it? > > thanks a lot for your help. > > Muriel > > -- Jacques Zylberg - Prof. B. Fischer's lab Chemistry Department Bar-Ilan University Ramat-Gan, Israel e-mail: zylbergj(a)noamy.ch.biu.ac.il Phone: +972-3-5317785

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randomize...why do it ??
by Himanshu Grover 21 Jul '04

21 Jul '04

hi, I was just wondering why it is required to randomize the coordinates of initial model or may be rotate their dihedrals before running the optimization routine (VTFM)... how would the results be affected if i don't randomize?? Actually, my resulting structure becomes worse if i randomize and then optimize rather than directly optimizing. any suggestions?? Secondly, I am not able to use rotate_dihedrals command somehow... it gives an error. if anyone knows how to use it, please tell me what all changes are required to be made before I use this command. The default *.top files give an error at the call, if I just change RAND_METHOD = randomize_dihedrals in __defs.top, and leave everything else as it is. this is an abstract of my log file which shows the segment generating error. ------------------**********------------------------- rotate__517_> Local optimization around Phi setodih_515_> Residues,dihedral type,all-selected,optimized: 605 2 604 574 rotate__517_> Local optimization around Psi chgidih_247E> Internal error: recover____E> ERROR_STATUS >= STOP_ON_ERROR: ------------------**********------------------------- is there anything that I am missing?? yours sincerely, Himanshu Grover

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core dumped when reading my restraint file
by daniele bemporad 21 Jul '04

21 Jul '04

Hi all When in my .top file I include: # Redefine the rd_restraints routine: SUBROUTINE ROUTINE = 'rd_restraints' # This is the default homology-derived restraints: READ_RESTRAINTS FILE = CSRFILE , ADD_RESTRAINTS = off # This is the additional user provided file: READ_RESTRAINTS FILE = 'my_restraint.rsr' , ADD_RESTRAINTS = on SET ADD_RESTRAINTS = off RETURN END_SUBROUTINE modeller dies with no message and dumps a core. It seems to read my_restraint.rsr , because if I introduce mistakes in the format they are recognised and also because the lines in my_restraint.rsr are present in the core file. I tried to locate: READ_RESTRAINTS FILE = 'my_restraint.rsr' , ADD_RESTRAINTS = on into the "special_restraints" subroutine, but the result is still that modeller dies and dumps a core. I have noticed that if I write "READ_RESTRAINTS FILE = 'my_restraint.rsr' " without "ADD_RESTRAINTS = on" then everything works fine. But as far as I understand the program, this would make modeller forget about the homology-derived restraints, wouldn't it ? Am I making some stupid mistake ? Is there a problem with my compilation or with this version of the program ? Any help is greatly appreciated. Many thanks Daniele __________________________________ Do you Yahoo!? Vote for the stars of Yahoo!'s next ad campaign! http://advision.webevents.yahoo.com/yahoo/votelifeengine/

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