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

James Starlight jmsstarlight at gmail.com
Mon May 16 02:58:57 PDT 2016


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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>>



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