April 2012 - IMP-users

Regarding IMP run
by subhomoi borkotoky 26 Apr '12

26 Apr '12

Dear all, I have the IMP to my Ubuntu 11.10 system. But I don't know how to use it even though I looked into IMP<http://salilab.org/imp/nightly/doc/html/namespaceIMP.html>Documentation . Please let me know how can I run the example scripts. what command should I write in terminal. Please help me. -- Thanks and Regards, -------------------------- SUBHOMOI BORKOTOKY, Centre for Bioinformatics Pondicherry University Pondicherry

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protein structure from amino acid sequences with IMP
by Adhikari, Badri (MU-Student) 13 Apr '12

13 Apr '12

Hello all, I am configuring IMP as non-root user in 3 of our redhat servers. My goal, for now, is to generate extended chain structures from amino acid sequences. I am able to run the following test examples that come with the IMP installation (credit goes to Ben and Daniel): i) test_charmm_atom.py ii) test_charmm_parameters.py iii) test_charmm_topology.py However, I am unable to run the examples in http://salilab.org/imp/nightly/doc/html/atom_examples.html#charmm_forcefield The most useful example for me would be structure-from-sequence. I get the following errors: $ python /rose/space1/imp/examples/structure-from-sequence.py Traceback (most recent call last): File "/rose/space1/imp/examples/structure-from-sequence.py", line 4, in <module> topology = IMP.atom.CHARMMTopology(IMP.atom.get_all_atom_CHARMM_parameters()) AttributeError: 'module' object has no attribute 'get_all_atom_CHARMM_parameters' $ python /rose/space1/imp/examples/charm-forcefield.py Traceback (most recent call last): File "/rose/space1/imp/examples/charm-forcefield-atom.py", line 10, in <module> ff = IMP.atom.get_heavy_atom_CHARMM_parameters() AttributeError: 'module' object has no attribute 'get_heavy_atom_CHARMM_parameters' $ python /rose/space1/imp/examples/molecular-hierarchy.py residue #16 of name "LYS"Added particle for 0...1 It looks like we need to supply the charm forcefield related files as well. I am wondering on the following questions as google does not seem to be helpful. (1) What file/files and parameter file/files do we need to run these examples? (2) Where do we place the files? (3) How to generate those files for the sequences that I have? Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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protein structure generation from sequences with IMP
by Adhikari, Badri (MU-Student) 10 Apr '12

10 Apr '12

Hello all, We are working on a project in which we need to generate protein models from the amino acid sequences, using IMP. After reading on the IMP website, I can see that this tool primarily deals with different data sources. But, still I believe that this tool could be useful for us as we might need to add more information later. Have you ever tried generating models (like pdb files) with just amino acid sequences using IMP? If you have anything that could be helpful to me please help. Warm Regards, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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Python wrapper error after IMP installation
by Adhikari, Badri (MU-Student) 10 Apr '12

10 Apr '12

Hello all, We installed IMP in one of our servers by building the source code files. I do not have root access on the servers. It looks like I need to use the atom module and so after installation, I tested the installation with the files in the test directory inside the atom module's directory. I can run the files like test_bd.py and test_charmm_atom.py run smooth, but files like test_charmm_parameters.py throw the following error. RuntimeError: Unknown error caught by Python wrapper Details of the error message is attached. Please help! Warm Regards, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri Cell: 573 639 2847 BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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