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@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@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@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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users