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@mail.missouri.edumailto:BAP54@mail.missouri.edu