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

[Eric Pettersen]

Hi Gleb,
	If you are using Gromacs 5 trajectories, you have to be using at least version 1.10.2 of Chimera.  If you are using that version (or later), please use “Report a Bug” in Chimera’s Help menu to file a bug report and attach your topology file to the bug report.  Thanks!

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On May 13, 2016, at 1:46 AM, James Starlight <jmsstarlight at gmail.com> wrote:
> 
> 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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