I am new to the imp-users mailing list. 

I am having trouble running PMI. I am following the online RNA Polymerase example (http://integrativemodeling.org/2.5.0/doc/manual/rnapolii_stalk.html) and adapting it to suit my own protein complex. 

When I run the modeling.py script, I seem to get as far as defining my x-links, then the program optimizes floppy bodies, lists all my proteins, then crashes. 

The crash takes place with the following error;

(after x-linking information)

Generating a NEW crosslink restraint with an uniqueID 45

--------------

ISDCrossLinkMS: generating cross-link restraint between

ISDCrossLinkMS: residue 89 of chain mol1d and residue 559 of chain mol2c

ISDCrossLinkMS: with sigma1 1.000000 sigma2 1.000000 psi 0.05

ISDCrossLinkMS: between particles mol1d_89_pdb and mol2c_536-585_bead_floppy_body_rigid_body_member

==========================================

optimize_floppy_bodies: optimizing 49 floppy bodies

mol2a_1

mol2a_2

mol2a_3

mol2a_4

mol1b_1

mol2c_1

mol2c_2

mol2c_3

mol2c_4

mol1d_1

mol3_1

mol3_2

mol4f

mol4g

mol4h

mol4i

mol4j

mol4k

mol4l

mol4m

will scale target mass by 454684.664

    mass_scale=target_mass_scale)

  File "/usr/local/lib/IMP-python/IMP/isd/gmm_tools.py", line 29, in decorate_gmm_from_text

    weight=float(fields[2])

IndexError: list index out of range

WARNING  Object "linker_restraints" was never used. See the IMP::Object documentation for an explanation.

Can anyone advise me what the issue here is? Does it relate to my target GMM file? 

I am at a loss. 

Yours,

Jason