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

[Ben Webb <>]

On 04/12/2012 01:59 PM, Adhikari, Badri (MU-Student) wrote:
> 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'
...
> It looks like we need to supply the charm forcefield related files

No, this error is complaining that there's a missing function in the 
IMP.atom module - it hasn't got as far as actually calling it at this point.

test_charmm_parameters.py calls the same functions, and you say that 
works, so they are definitely there (and so are the force field files). 
It looks like when you run the examples, something in IMP is broken. Are 
you sure you don't have two copies of IMP installed?

	Ben
--
                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle