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.edu