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

James Starlight jmsstarlight at gmail.com
Mon May 16 03:13:19 PDT 2016


something relevant in my model:

this is martini CG model consisted of big membrane protein and small
water soluble protein. In my particular trajectory I have only atoms
of both proteins recognized by chimera as individual chains (e.g small
protein is chain A and the biggest is consisted of chains B-N).

Gleb

2016-05-16 11:58 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
> update:
>
> with the up-to-date chimera Trajectory is loaded fine
> now the question is related to the analysis of the binding interface.
> is it possible to make contact maps plots based on the 2 selections
> from the input trajectory assuming that I am using martini CG model?
>
> Gleb
>
> 2016-05-16 10:39 GMT+02:00 James Starlight <jmsstarlight at gmail.com>:
>> OK will try to update Chimera today !
>>
>> What chimera's tools could be useful for the contact map based
>> analysis of md trajectories related to my case ? E.g to determine
>> binding interface between 2 proteins from long md simulation.
>>
>> Gleb
>>
>> 2016-05-13 19:52 GMT+02:00 Eric Pettersen <pett at cgl.ucsf.edu>:
>>> 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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