July 2004 - modeller_usage

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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Re: [modeller_usage] Restraints Problem
by akshay17 20 Jul '04

20 Jul '04

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. Thanks Akshay Patny. > On Fri, Jul 16, 2004 at 04:41:03PM -0500, akshay17 wrote: > > I recently joined Modeller mailing list and i am also > > new to the program. > > > > I am using Modeler as an interface from Insight II. I > > have been trying to give my own restraints during the > > model generation as a .rsr file. I tried using both the > > MODELER FORMAT as well as the USER FORMAT restraint > > files. The problem is whenever i submit my job, it does > > not complete and gives error in log file one of which is > > the following: "Incorrect record identifier in restraint > file; card:" > > You have blank lines in your restraints file; Modeller6v2 > doesn't understand these. Take them out and all should be > well. > > 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 [Attachment: Constraints_USER.rsr] 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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RMS and DRMS functions of COMPARE again
by Binbin Liu 19 Jul '04

19 Jul '04

Hello, just have to make my question more detailed. I would like to calculate RMSD for ALL ATOMS between template and the models. Binbin -- Binbin Liu Bioinformatics Ph.D student School of Biomedical Sciences University of Leeds, Leeds,LS2 9JT England, UK Phone: (44)113 343 3072 Email: bmbbl(a)bmb.leeds.ac.uk

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RMS and DRMS functions of COMPARE
by Binbin Liu 19 Jul '04

19 Jul '04

Hello there, 'compare' can be used to calculate the RMSD between the template and models. In general, during homology modelling, there can be residues mutated in the sequence alignment so that the different numbers of atoms are superimposed in Catesian space. I wonder how MODELLER work out the RMSD under this situition? Thanks a lot. Binbin -- Binbin Liu Bioinformatics Ph.D student School of Biomedical Sciences University of Leeds, Leeds,LS2 9JT England, UK Phone: (44)113 343 3072 Email: bmbbl(a)bmb.leeds.ac.uk

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loop positioning
by John Simms 17 Jul '04

17 Jul '04

Hi All, A quick question. I have a pair of beta strands in a GPCR. Experimental evidence suggests that the distal portion (2nd beta strand of the loop lies underneath the proximal part of the loop (1st beta strand). I have used modeller to model this region , but all of the models have the distal part ontop of the proximal part :-(. Does anyone know how I can restrain the orinetation of the loop fragments so that the start of the loop is ontop of the end on the loop. Thanks again John

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Error: Array too small. Increase MAXBND
by K S Doctor 16 Jul '04

16 Jul '04

How do I deal with the following error: getf____223E> Array too small. Increase MAXBND current maximum, current need: 6180 6181 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 I am running a 479 AA protein + a HETATM (NAG or "1") which is described in /modlib/restyp.lib I have had no problem running the dimer 479 AA * 2 , but without the HETATM. I am attaching the top file and representative ali, the PDB is the public one. Simply setting SET MAXBND = 6181 in the TOP file did not work (error) thanks, Kutbuddin @ The Burnham Institute - SD, CA ;1ew2monomer >P1;1EW2_A structureX:1ew2_A:1:A:::PLAP:Homo sapien:: IIPVEEENPDFWNREAAEALGAAKKLQPAQTAAKNLIIFLGDGMGVSTVTAARILKGQKK DKLGPEIPLAMDRFPYVALSKTYNVDKHVPDSGATATAYLCGVKGNFQTIGLSAAARFNQ CNTTRGNEVISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVPASARQ EGCQDIATQLISNMDIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLDGKNLVQEWLAK RQGARYVWNRTELMQASLDPSVTHLMGLFEPGDMKYEIHRDSTLDPSLMEMTEAALRLLS RNPRGFFLFVEGGRIDHGHHESRAYRALTETIMFDDAIERAGQLTSEEDTLSLVTADHSH VFSFGGYPLRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLKDGARPDVTESESGSPEYR QQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQTFIAHVMAFAACLEPYTACDLAPP/ 1* >P1;1ew2_delta sequence:1ew2_delta:::::::: IIPVEEENPDFWNREAAEALGAAKKLQPAQTAAKNLIIFLGDGMGVSTVTAARILKGQKK DKLGPEIPLAMDRFPYVALSKTYNVDKHVPDSGATATAYLCGVKGNFQTIGLSAAARFNQ CNTTRGNEVISVMNRAKKAGKSVGVAAAARVQHASPAGTYAHTVNRNWYSDADVPASARQ EGCQDIATQLISNMDIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLDGKNLVQEWLAK RQGARYVWNRTELMQASLDPSVTHLAAAAEPGDMKYEIHRDSTLDPSLMEMTEAALRLLS RNPRGFFLFVEGGRIDHGHHESRAYRALTETIMFDDAIERAGQLTSEEDTLSLVTADHSH VFSFGGYPLRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLKDGARPDVTESESGSPEYR QQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQTFIAHVMAFAACLEPYTACDLAPP/ 1* # default model INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'monomer_v4.ali' # alignment filename SET KNOWNS = '1EW2_A' # codes of the templates SET SEQUENCE = '1ew2_delta' # code of the target 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) SET HETATM_IO = on # SET WATER_IO = off # ;SET MAXBND = 6181 # based on output log need CALL ROUTINE = 'model' # do homology modelling

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