July 2004 - modeller_usage

Restraints Problem
by akshay17 16 Jul '04

16 Jul '04

Dear Sir 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:" I am attaching my .top file, restraints file and also the log file here. Please suggest me to fix this problem. I will be glad. Thanks Akshay Patny 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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(no subject)
by karl schweighofer 16 Jul '04

16 Jul '04

Hello, I am trying to protonate at ADP molecule with modeller6. THe ADP residue is specified in the library, but I keep getting this error: gener___479E> Must not use patching residues here. Residue type index, residue type: 33 # recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Here is the script for the protonation: # This will read a specified atom file, generate all hydrogen atoms, # add atomic radii and charges, and write the model to a PDB file in # the GRASP format. This can be used with GRASP to display electrostatic # properties without assigning charges and radii in GRASP. INCLUDE SET TOPLIB = '$(LIB)/TOP.LIB' SET PARLIB = '$(LIB)/PAR.LIB' READ_TOPOLOGY FILE = '$(LIB)/TOP.LIB' READ_PARAMETERS FILE = '$(LIB)/PAR.LIB' SET TOPOLOGY_MODEL = 1, HYDROGEN_IO = on, HETATM_IO = on, WATER_IO = on SET ATOM_FILES_DIRECTORY = './' # directories for input atom files READ_MODEL FILE = 'adp.pdb' RENAME_SEGMENTS SEGMENT_IDS = 'A' SEQUENCE_TO_ALI ATOM_FILES = 'adp', ALIGN_CODES = 'adp' SEQUENCE_TO_ALI ADD_SEQUENCE = on, ATOM_FILES = ATOM_FILES 'adp.pdb', ; ALIGN_CODES = ALIGN_CODES 'adp' GENERATE_TOPOLOGY SEQUENCE = 'adp' TRANSFER_XYZ BUILD_MODEL INITIALIZE_XYZ = off, BUILD_METHOD = 'INTERNAL_COORDINATES' WRITE_MODEL FILE = 'protoadp.pdb', MODEL_FORMAT = 'GRASP' And here is the ADP PDB File: HETATM 569 PB ADP X 68 14.423 48.400 0.539 HETATM 570 O1B ADP X 68 15.523 47.578 -0.057 HETATM 571 O2B ADP X 68 14.303 48.106 2.067 HETATM 572 O3B ADP X 68 14.698 49.918 0.358 HETATM 573 PA ADP X 68 11.796 47.376 0.153 HETATM 574 O1A ADP X 68 12.031 45.921 0.312 HETATM 575 O2A ADP X 68 11.228 48.083 1.373 HETATM 576 O3A ADP X 68 13.146 48.057 -0.376 HETATM 577 O5' ADP X 68 10.874 47.635 -1.110 HETATM 578 C5' ADP X 68 11.196 47.105 -2.379 HETATM 579 C4' ADP X 68 10.286 47.636 -3.486 HETATM 580 O4' ADP X 68 9.080 46.895 -3.526 HETATM 581 C3' ADP X 68 9.861 49.060 -3.289 HETATM 582 O3' ADP X 68 9.602 49.725 -4.510 HETATM 583 C2' ADP X 68 8.559 48.875 -2.526 HETATM 584 O2' ADP X 68 7.781 49.993 -2.657 HETATM 585 C1' ADP X 68 7.956 47.654 -3.193 HETATM 586 N9 ADP X 68 7.087 46.896 -2.257 HETATM 587 C8 ADP X 68 7.503 45.956 -1.333 HETATM 588 N7 ADP X 68 6.392 45.519 -0.679 HETATM 589 C5 ADP X 68 5.314 46.174 -1.216 HETATM 590 C6 ADP X 68 3.977 46.114 -0.937 HETATM 591 N6 ADP X 68 3.529 45.338 0.072 HETATM 592 N1 ADP X 68 3.138 46.928 -1.662 HETATM 593 C2 ADP X 68 3.573 47.780 -2.658 HETATM 594 N3 ADP X 68 4.896 47.853 -2.965 HETATM 595 C4 ADP X 68 5.741 47.039 -2.222 Any ideas why this won't work? Thanks kindly, Karl Schweighofer karl(a)mail.arc.nasa.gov

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pseudo-atom usage?
by Daniel Rigden 16 Jul '04

16 Jul '04

Hi all Can anyone help with an example of the use of additional restraints involving pseudoatoms? I've read the relevant sections of the manual http://salilab.org/modeller/manual/node99.html http://salilab.org/modeller/FAQ.html#8 and it's still not clear to me. The FAQ has this example of a user-added restraint SET ATOM_IDS 'CA:35:A' 'CA:40:A' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 10.0 0.1 How to define pseudo-atoms instead of single real atoms? Alternatively, if the restaint were added in a file, how to specify defined pseudo-atoms within the format? R Form Modality Feature Group Numb_atoms Numb_parameters 0 Atom_indices Parameters R 3 1 1 1 2 2 0 437 28 1.5000 0.1000 In my case, I'd like to make a helix (which I'll define as a pesudoatom) in a large insertion pack better, more compactly against the rest of the protein. Has anyone any experience with similar situations? Many thanks in advance Daniel Rigden -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4414 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.

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MODELLER file archive
by Modeller Caretaker 16 Jul '04

16 Jul '04

In response to user requests, I have created a MODELLER file archive, from where you can download example TOP scripts. I will be adding examples to this archive on an occasional basis, some of which will probably find their way into future releases of MODELLER. Of course, it wouldn't be much use without user-contributed examples; there are instructions on the page on how to send example files to me for inclusion. You can find the archive at: http://salilab.org/modeller/archive.shtml Enjoy! Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mailing list: http://salilab.org/mailman/listinfo/modeller_usage

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modeller problem
by shantanu gautam 15 Jul '04

15 Jul '04

Dear sir/madam, I am doing research at IIT Kharagpur on modeling retrotransposable genes. I faced severe problem while running Widows based modeller version. The steps I had followed for running modeller is 1) generated alignment file as .ali file 2) generated pdb display file and structure file as pdb format. 3) Model-default 4) Then I run the modeller from the command prompt but after giving mod.bat model-default.top it was showing error Len,string: D:\sh\modeller6v2\bin\sg\\ 5) The folder containing the modeller is sh and sg is folder in which we are working. Please let me know how to work out this problem. We will be greatly thankful for your kind cooperation. Thanking you. Yahoo! India Careers: Over 65,000 jobsonline.

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soaking in aqueous medium...
by Himanshu Grover 15 Jul '04

15 Jul '04

Hi, I wish to know if it is possible to soak a spherical region of a protein molecule in aqueous medium before doing the Simulated Annealing refinement using modeller. If anyone has done this before, please apprise me of the involved steps. thanks, yours sincerely Himanshu

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announcing normal mode analysis web server ElNemo
by Karsten Suhre 15 Jul '04

15 Jul '04

Deal Modeller-users, I thought that some of you might be interested in our new protein normal mode analysis web-server ElNemo. A particular interesting application of normal modes in the context of homology modelling is the possibility to generate a large spectrum of templates having different conformations. ElNemo is available at: http://igs-server.cnrs-mrs.fr/elnemo/ A paper describing its functions has just been published in the NAR web-server issue: http://nar.oupjournals.org/cgi/content/full/32/suppl_2/W610 (This paper is open access) I hope that you will find this web server useful and I would be happy about any comments or suggestions, Kind regards, Karsten. ---- ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement Normal mode analysis (NMA) is a powerful tool for predicting the possible movements of a given macromolecule. It has been shown recently that half of the known protein movements can be modelled by using at most two low-frequency normal modes. Applications of NMA cover wide areas of structural biology, such as the study of protein conformational changes upon ligand binding, membrane channel opening and closure, potential movements of the ribosome, and viral capsid maturation. Another, newly emerging field of NMA is related to protein structure determination by X-ray crystallography, where normal mode perturbed models are used as templates for diffraction data phasing through molecular replacement (MR). Here we present ElNémo, a web interface to the Elastic Network Model that provides a fast and simple tool to compute, visualize and analyse low-frequency normal modes of large macro-molecules and to generate a large number of different starting models for use in MR. Due to the ‘rotation-translation-block’ (RTB) approximation implemented in ElNémo, there is virtually no upper limit to the size of the proteins that can be treated. Upon input of a protein structure in Protein Data Bank (PDB) format, ElNémo computes its 100 lowest-frequency modes and produces a comprehensive set of descriptive parameters and visualizations, such as the degree of collectivity of movement, residue mean square displacements, distance fluctuation maps, and the correlation between observed and normal-mode-derived atomic displacement parameters (B-factors). Any number of normal mode perturbed models for MR can be generated for download. If two conformations of the same (or a homologous) protein are available, ElNémo identifies the normal modes that contribute most to the corresponding protein movement. The web server can be freely accessed at http://igs-server.cnrs-mrs.fr/elnemo/index.html. -- Karsten Suhre Charge de Recherche CNRS (Research Scientist) Information Genomique & Structurale UPR CNRS 2589 31, chemin Joseph Aiguier F-13402 Marseille Cedex 20 Tel: ++33.4.91.16.46.04 Sec: ++33.4.91.16.45.48 Fax: ++33.4.91.16.45.49 mailto:Karsten.Suhre@igs.cnrs-mrs.fr http://igs-server.cnrs-mrs.fr/~suhre

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distance-dependent dielectric const.??
by Himanshu Grover 14 Jul '04

14 Jul '04

Hi ppl., Is the distance-dependent dielectric constant being considered under modeller refinement scheme?? if yes, where is the default parameter defined...?? yours sincerely

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modeller as an optimizer, not as a modeller??
by Himanshu Grover 14 Jul '04

14 Jul '04

hellow, i wish to know whether modeller can be used as a general optimization tool. I have a structure of my protein... also know its binding site to another protein (its a protein-protein complex). i just want to apply simulated annealing to the binding site of my model, to find the best binding conformation... can modeller do that for me?? regarding the same, please apprise me of some details... firstly, do i need to use the restraints generated by modeller... if yes, which ones?? secondly, what new restraints, if at all, should be applied(as a part of special restraints). thirdly,is it necessary to use homology basis, the alignment, templates, and homology derived restraints...?? if anyone could give me a sample top script as to how the problem can be tackled, it would be a great help... moreover, any other nuances/suggestions in the approach would be appreciated... thanks very much, sincerely, himanshu

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[Fwd: [modeller_usage] beta strand restriction]
by John Penniston 14 Jul '04

14 Jul '04

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