[IMP-users] protein structure from amino acid sequences with IMP

["Adhikari, Badri (MU-Student)" <>]

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

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