VMD-L Mailing List
From: liushiyong (liushiyong_at_gmail.com)
Date: Thu Dec 20 2018 - 04:36:04 CST
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On 12/20/2018 17:18,Александр Кошкаров<steuermannako@gmail.com> wrote:
Dear all,I faced a problem analyzing a protein in dimeric form with Dynamical Network Analysis implemented inVMD. When I follow the tutorial with aaRS:tRNA complex, everything works well. Moreover, it's Okwhen I use a monomer of my protein. The problem is rising when I use the homo-dimer and is that nodynamical network appears in the second subunit, while in the first one it exists. Visualization of thetrajectory after NetworkSetup disturbs both covalent bonds in the second subunit although all theatoms are in correct position (in correspondence with those of the first subunit) and its dynamicalnetwork (a few nodes and no connections are shown).I got a trajectory with GROMACS. All the residues in two subunits had different numbers. The topologytopol.top file was constructed using gmx2pdb with a -merge flag to avoid the appearing of #include linksin the topology file. When using catdcd, the .xtc trajectory was converted to .dcd. Topology file wasconverted using the top2psf.pl script by Mark Baaden. Converted topology and trajectory were used forDynamical Network Analysis.Which step could be incorrect?How to build the dynamical network between two subunits in the dimer?Any help and suggestions are very appreciated.best regards,Koshkarov Alexandr.
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