- modeller_usage - salilab.org

** MODELLER Support ** TEST PLEASE IGNORE
by Bozidar Jerkovic 18 Feb '02

18 Feb '02

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mkspline_E
by Luca Settimo 18 Feb '02

18 Feb '02

Dear modeller, I was using still modeller 4 (just to complete one work that I was doing) I have one problem, I m building a model using 7 templates (I made a structural alignment that I am using to build my model). Everything works fine... except that for one situation (so my input file top and ali are correspondent, except the sequence that I have to model... like you can immagine) and I have this message: mkspline_E> too many parameters, increase MPRMCNS if I remove one template it works fine... what does it mean this message? how can I still use 7 templates? Luca ................................................................... Luca Settimo Molecular Structures and Biocomputing Department of Biochemistry and Pharmacy Åbo Akademi University Tykistökatu 6A 20520 Turku Finland phone: +358 (0) 2 2154600 fax: +358 (0) 2 2153280 mobile phone: +358 50 5238418 mailto:lsettimo@abo.fi http://www.abo.fi/~lsettimo

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bug report
by vuissoz Jean-Marc 16 Feb '02

16 Feb '02

dear modeller team, Probably something is not installed correctly on my version of modeller6.1 but I don't find what, here are the log files en top files with the error reported. best tanks vuissoz jean-marc >P1;1fdx sequence:1fdx:1 : :54 : :ferredoxin:Peptococcus aerogenes: >2.00:-1.00 AYVINDSCIACGECPVNIIQGSIYAIDADSCIDCGSCASVCPVGAPNPED* SET SEARCH_RANDOMIZATIONS = 100 SET FILE = 'prot.ali' SEQUENCE_SEARCH ALIGN_CODES = '1fdx', DATA_FILE = ON MODELLER 6v1, 17 Jan 2002 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2002 Andrej Sali All Rights Reserved Written by A. Sali with help from A. Fiser, R. Sanchez, M.A. Marti-Renom, B. Jerkovic, A. Badretdinov, F. Melo, J.P. Overington & E. Feyfant Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, IRIX64 IRIS 6.5 IP30 Date and time of compilation : 01/25/2002 20:36:35 Job starting time (YY/MM/DD HH:MM:SS): 2002/02/15 17:44:24.629 read_se_367E> Sequence not found; code: P1;1xnb recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 2306323 2252.269 2.199 Starting time : 2002/02/15 17:44:24.629 Closing time : 2002/02/15 17:44:33.146 Total CPU time [seconds] : 0.00

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strand restraints
by Reuter Nathalie 15 Feb '02

15 Feb '02

Dear modellers, we use Modeller6 and we have some problems restraining beta-sheets in our model. The student working on this project sent an -email to the forum a few days ago and since then we have tried many different things to try to analyze the problem so we send more precise questions. We tried to restrain beta strands in our model, using the RESTRAINT_TYPE = 'SHEET' or RESTRAINT_TYPE = 'STRAND' . All our tests were unsuccessful. Last thing we tried was to force beta strands in the model to be longer than they are without special restraints. That means, in the previous model, there are beta strands (they exist in the template structure) without adding other special restraints in the top script. I thus think it should be possible to make them slightly longer. But if I try to apply special restraints to increase their length, the strands completely disappear in the models. The .top file is OK, modeller can read it, there are no error messages in the .log file, the .rsr file contains additionnal restraints (dihedral pairs) with regards to the same calculation without any restraint. The .V files are also different with or without the special restraints. So everything seems to be OK, but the models never contain these additionnal beta strands. The longer the strands we try to restrain, the more violations (in the log file) there are but their magnitude is not significantly higher than when I apply an 'alpha' restraint (which works perfectly well, i.e. it appears in the model whatever the region we try to introduce it in). To force strand (or even beta-sheets) never worked. So it looks like restraining strands and beta-sheets is much more difficult than alpha-helices, which we can introduce almost anywhere in the model. Here are our questions : Is it normal to be able to force an alpa helix wherever you want and not a beta, and if yes why ? Are the violations due to beta strands too penalizing ? Shall we modify the optimization schedule and if yes, which parameters should we change ? Is it possible to exclude block of atoms from the optimization procedure of the objective function ? Thanks, Nathalie Reuter -- Nathalie REUTER, PhD U.410 INSERM Faculte de medecine Xavier Bichat 16, rue Henri Huchard BP 416 75870 PARIS Cedex 18 tel : (33) 01.44.85.61.32 fax : (33) 01.42.28.87.65 -- Nathalie REUTER, PhD U.410 INSERM Faculte de medecine Xavier Bichat 16, rue Henri Huchard BP 416 75870 PARIS Cedex 18 tel : (33) 01.44.85.61.32 fax : (33) 01.42.28.87.65

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How to model DNA binding protein
by Michael Buck 14 Feb '02

14 Feb '02

How can I include the DNA structure when modelling a DNA binding protein? Can I just include the HETATM atoms using SET MODEL_TOPOLOGY = 1, HETATM_IO = on This doesn't seem to work, what else to need to include? Michael Buck ************************************************ Michael Buck NCSU Genetics mjbuck(a)unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************

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errror in .log
by Giulio Rastelli 14 Feb '02

14 Feb '02

Dear modellers, I was wondering what the meaning of this error message is: splinel_223E> Array too small. Increase MPRMCNS current maximum, current need: 990900 990926 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Thanks, Giulio Giulio Rastelli Dipartimento di Scienze Farmaceutiche Universita di Modena e Reggio Emilia Via Campi 183 41100 Modena - ITALY ------------------------------------- tel 0039-059-2055145 fax 0039-059-2055131 -------------------------------------

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Re: Modelling Heme
by Roberto Sanchez 13 Feb '02

13 Feb '02

It is possible to transfer the heme group from the template to the target (model) using a "block" residue as suggested by Andras. But as Christoph pointed out the heme residue type is defined in the Modeller topology libraries, and the corresponding parameters are present in the parameter libraries. So (in theory) all you need to know is how to refer to the HEME residue in the alignment file. This you can figure out by looking at Modeller's residue type library (restyp.lib) where you will find the entry: 31 | HEM | h | HEME | heme ligand this tells you that Modeller uses 'h' as the one-letter code for the HEME residue. Now all you need to do is add the 'h' residues in the right places of your template and target sequences in the alignment, add "SET HETATM_IO = on" to the TOP file, cross you fingers, and re-run Modeller. If all is fine the heme group will appear in your model. The difference between this approach and using a block residue is that the block residue is treated as a rigid object that is just copied from the template to the model, for example Modeller can not distort the block residue and the rest of the protein does not "feel" its presence beyond the protein - block residue distance restraints extracted from the template. This limitation dissapears when defining the heme group as a proper residue. I hope this helps. Best, Roberto -- Roberto Sanchez, Assistant Professor Structural Biology Program, Department of Physiology & Biophysics and Institute for Computational Biomedicine, Mount Sinai School of Medicine Box 1677, 1425 Madison Avenue, New York, NY 10029 phone +1 (212) 659 8648, fax +1 (212) 849 2456 http://physbio.mssm.edu/~sanchez/ ----- Original Message ----- From: fisera <fisera(a)rockefeller.edu> Date: Thursday, February 14, 2002 1:12 am Subject: Re: Modelling Heme > > please follow instructions from FAQ (Freq. Asked Questions) point 16, > Modeller manual > > http://salilab.org/modeller/manual/node29.html > > good luck > Andras > > > Christoph Nimptsch wrote: > > > > Dear Modellers, > > > > I am trying to model a protein containing a heme group. > > There is a residue type called heme in top_heav.lib, but I don`t > know how to > > utilize it. > > I am aware of changing my alignment to include HETATMs but I haven`t > > succeeded yet. > > > > Do I have to change the pdb-templates to include the heme > residue? How can I > > make it clear that MODELLER 6v1 should use it? > > > > Is it possible to receive the model with the heme group in it? > > > > Thanks for any suggestions, > > > > Christoph Nimptsch >

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Modelling Heme
by Christoph Nimptsch 13 Feb '02

13 Feb '02

Dear Modellers, I am trying to model a protein containing a heme group. There is a residue type called heme in top_heav.lib, but I don`t know how to utilize it. I am aware of changing my alignment to include HETATMs but I haven`t succeeded yet. Do I have to change the pdb-templates to include the heme residue? How can I make it clear that MODELLER 6v1 should use it? Is it possible to receive the model with the heme group in it? Thanks for any suggestions, Christoph Nimptsch

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restraints on beta strands
by Juliette Martin 13 Feb '02

13 Feb '02

I m building a protein with a template of relatively low identity score, but good HCA alignement . I want to restraint parts of my protein to be in beta strands. I tried SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '60' '64' MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '71' '76' RETURN END_SUBROUTINE and SUBROUTINE ROUTINE = 'special_restraints' SET ADD_RESTRAINTS = on MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '60' '64' MAKE_RESTRAINTS RESTRAINT_TYPE = 'strand', RESIDUE_IDS = '71' '76' MAKE_RESTRAINTS RESTRAINT_TYPE = 'SHEET', ATOM_IDS = 'N:60' 'O:76', SHEET_H-BONDS = -5 RETURN END_SUBROUTINE in the top file, but beta strands are not in any of my models, nor it is in the structure .ini . Is it possible that the restraint is too 'heavy' for the molecule?

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** MODELLER Support ** Docking with modeller ?
by Bozidar Jerkovic 12 Feb '02

12 Feb '02

Dear Roman, In theory YES. Is it useful? It depends how much time and effort you want to invest in it. Please take a look at FAQs 8-12, to see how you can add restrains manually. Also we encourage people to post questions to MODELLER list directly, so that other members of the community can benefit from this correspondence. Lep pozdrav, Bozidar -----Original Message----- From: Roman Jerala [mailto:roman@hp14.cmm.ki.si] Sent: Tuesday, February 12, 2002 3:55 PM To: bozidar(a)salilab.org Subject: Docking with modeller ? Dear Bozidar, can you tell me if it is possible (and usefull) to use Modeller for docking or modelling complexes. In principle if restraints (such as NOEs or perhaps chemical shift changes, which are more "fuzzy") can be entered this should in principle drive the ligand to the correct position. With best regards, Roman ------------------------------------------------------- Asst. prof. Roman Jerala, PhD Laboratory for molecular modelling and NMR spectroscopy National Institute of Chemistry POB 660 Hajdrihova 19 SI-1000 Ljubljana SLOVENIA Tel: +386 1 476 0376 Fax: +386 1 476 0300 E-mail: roman.jerala(a)ki.si

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