[Chimera-users] Analysis of the contact maps from the MARTINI MD trajectory

James Starlight jmsstarlight at gmail.com
Fri May 13 01:46:32 PDT 2016


Dear Chimera users!


I am in charge with the analysis of protein-protein association during
long molecular dynamic simulation where my system was parametrized
using MARTINI CG force field. In particularly I am interesting to
find residues on one of the protein which are crustal for the binding
interface established during this MD.
For that purpose I am trying to use Chimera to load trajectory and
corresponded tpr file using MD movie plugin and than to
map contact maps produced by Gromacs onto the 3D structure using Chimera.
The problem that Chimera does not recognize properly the trajectory
and topology. Briefly I have removed all solvent from both files
before loading them to the Chimera using editconf and gmx convert-tpr
obtaining eventually trajectory and topology with the same number of
atoms.


Than when I load it to Chimera that is the error which MD movie sent me:

VERSION 5.0.2
using floats
version 100, generation 26
8 atoms
Traceback (most recent call last):
  File "CHIMERA/lib/python2.5/site-packages/Pmw/Pmw_1_3/lib/PmwBase.py",
line 1747, in __call__
  File "CHIMERA/share/chimera/baseDialog.py", line 328, in command
  File "CHIMERA/share/chimera/baseDialog.py", line 543, in OK
  File "CHIMERA/share/Trajectory/EnsembleLoader.py", line 92, in Apply
  File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line
56, in loadEnsemble
  File "CHIMERA/share/Trajectory/formats/Gromacs/__init__.py", line
67, in loadEnsemble
  File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 25,
in __init__
  File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line 86,
in __init__
  File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line
345, in _readTopology
  File "CHIMERA/share/Trajectory/formats/Gromacs/Gromacs.py", line
338, in _readString
  File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring
    raise EOFError
EOFError
EOFError

  File "CHIMERA/lib/python2.5/xdrlib.py", line 197, in unpack_fstring
    raise EOFError

See reply log for Python traceback.

Will be thankful for any suggestions!

Gleb


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