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May 2012

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IMP issue regarding examples in web-ste: this is probably an expert level issue
by Adhikari, Badri (MU-Student) 03 May '12

03 May '12

Hello IMP users and experts, IMP looks attractive to us. Thank you for all the active support. I am using IMP available at http://salilab.org/imp/get.php?pkg=1.0/download/imp-1.0.tar.gz Two interesting questions: 1. The example code at http://salilab.org/imp/nightly/doc/html/atom_examples.html#charmm_forcefiel… and the example at PREFIX/modules/atom/examples/charmm_forcefield.py are supposed to do the same thing, but the code are not exactly same. The web code uses functions that my IMP does not understand. Is this some IMP version issue? 2. The first example, access dope, in http://salilab.org/imp/nightly/doc/html/atom_examples.html tries to pick up 1fdx.B99990001.pdb which I don't find anywhere in any of the folders. So, how is this example supposed to run? Looks like this has something to do with my issues as well. Most importantly, please, help me find a version of code for http://salilab.org/imp/nightly/doc/html/atom_examples.html#structure_from_s… that is similar to the examples provided in the installation package. It looks like my version of IMP does not have functions like IMP.atom.get_all_atom_CHARMM_parameters(). I am not familiar enough with IMP's language to convert the code myself. I am desperately working on trying to generate some models from sequences. --------------------------------------------------------------------------------------------------- In case you think that it is some installation issues, here are the details: --------------------------------------------------------------------------------------------------- My IMP installation log is at http://web.missouri.edu/~bap54/IMPinstall.log I have installed IMP in two of our servers. I don't have root access in these machines. IMP seems to be working well for normal use because I can run almost all of the examples and test files. The list of programs that I can run are attached as list_of_programs_that_run_smoothly.txt However, I get error while executing some programs. The list is attached in programs_that_throw_error.txt Also, I cannot run examples at http://salilab.org/imp/nightly/doc/html/atom_examples.html#structure_from_s…. The errors that I receive are attached in errors_in_the_website_examples.txt The most important example that I need to run is http://salilab.org/imp/nightly/doc/html/atom_examples.html#structure_from_s…. And the error that I get while trying to run this example is: $python structure_from_sequence.py Traceback (most recent call last): File "../imp_examples/structure_from_sequence.py", line 4, in ? topology = IMP.atom.CHARMMTopology(IMP.atom.get_all_atom_CHARMM_parameters()) AttributeError: 'module' object has no attribute 'get_all_atom_CHARMM_parameters' * I have already tried in 3 different machines with different configurations, with no luck at all. In one virtual machine, I installed with root access as well. I get the same error everywhere. The interesting thing is: once installed nothing is written to share/doc/imp, so I need to manually copy the example files needed (like example_protein.pdb) to run the examples. * All required tools are installed properly. I worked hard to install all boost libraries. All the required programs are installed correctly. This can be seen in the IMPinstall.log at http://web.missouri.edu/~bap54/IMPinstall.log * I have single copy of IMP installed. No multiple copies. 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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