bwGRID

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Modeller

What is Modeller?

PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS

MODELLER is used for homology or comparative modeling of protein threedimensional structures (1). The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containining all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints (2,3), and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc.

University of California, San Francisco, USA | Rockefeller University, New York, USA | Harvard University, Cambridge, USA | Imperial Cancer Research Fund, London, UK | Birkbeck College, University of London, London, UK

URL: Modeller - Homepage

Download Modeller and License Information

Modeller Software is free for academic and non-profit users.

If you want to use Modeller on our bwGRID-HPC-System, please

... contact us using this email : rainer.rutka(at)uni-konstanz.de

... we will then contact the user with instructions for using CPMD on our cluster.

  • Modeller Latest Distribution : the actual distribution of Modeller we are running is: 9.10
    1. mod9.10 (main programm)
    2. mod9.10_x86_64-intel8 (main programm 64 bit)
    3. modpy.sh
    4. modslave.py
    5. env.sh
    6. __align_strs_seq.top
    7. __asgl_mod.top
    8. __cispeptide.top
    9. __cluster.top
    10. __complete.top
    11. __default_patches.top
    12. __defs.top
    13. __fit.top
    14. __full_homol.top
    15. __generate_model.top
    16. __getnames.top
    17. __homcsr.top
    18. __loop.top
    19. __model.top
    20. __mod.top
    21. __multiple_models.top
    22. __principal.top
    23. __refine.top
    24. __sequence_search.top
    25. __single_model.top
    26. __special.top
    27. __spline.top
    28. lib/python2.3/site.py

bwGRID Anpassungen / adaptations

bwGRID-Setups

Modeller

Description: Module - File (without license information) *
Path/Filename: /opt/bwgrid/chem/modeller/9.10/modulefiles/9.10

* bwGRID license is included in the orginal 'modules'-file.
If you need a new one, apply for the bwGRID license here: rainer.rutka(at)uni-konstanz.de

bwGRID examples

The PBS batch system can be used to manage the nodes allocation in a cluster of hosts. For example, using a particular job script, it's possible to communicate to the MPI launcher program (mpirun) the number and the list of nodes that PBS has allocated for the whole job as requested from the user. The PBS server will not run more jobs on the busy nodes until the end of the current job. Here is an example of a script to do this over our bwGRID network using a implementation of Open-MPI.

Description: bwGRID - Example PBS File for submitting a job via. 'qsub'
Path/Filename: /opt/bwgrid/chem/modeller/9.10/bwgrid_example/bw-grid-modeller-example.pbs
Description: Examples data file for bw-grid-modeller-example.pbs - file (included)
expand in /opt/bwgrid/chem/modeller/9.10
Path/Filename: /opt/bwgrid/chem/modeller/9.10/bwgrid-example-files.taz

© Copyright 1989-2011 Andrej Sali
Δ 20.12.2011 | initial version | rainer.rutka(at)uni-konstanz.de