Page AktinAnalysis

TODO
Person Task State
Martin calculation of electrostatic potential map of (closed_atp_dimer, closed_atp),( closed_adp_dimer, closed_adp) undone
Martin testing conditional state probabilities of simulation trajectories for convergence using HMM state definition (s-closed, closed, open) undone
Splette MD runs of actin trimers to obtain relaxed filament part undone
Splette calculation of 'mean' trimer structures which will serve as a basis for binding energy calculations undone
Martin binding energy calculations of closed_atp/closed_adp/superclosed_atp trimer undone

Analysis Protocol

  • Analysis of state trajectories
    • equidistant discretization of state coordinate using 150 boxes
    • computation of transition matrix based on discretized trajectory
    • determining number of clusters (noc) by considering eigenvalues of transition matrix which are greater than 0.9
    • run HMMGaussian to determine noc clusters in state coordinate
    • resulting clustering is displayed in first figure of each trajectory (x axis shows time, y axis distance, coloring indicates clustering)
    • cluster indices over time can be found in clustered.tar.gz

  • Analysis of depth trajectories
    • equidistant discretization of depth coordinate using 150 boxes
    • computation of transition matrix based on discretized trajectory
    • determining number of clusters (noc) by considering eigenvalues of transition matrix which are greater than 0.8
    • run HMMGaussian to determine noc clusters in depth coordinate
    • resulting clustering is displayed in second figure of each trajectory (x axis shows time, y axis inversed depth, coloring indicates clustering)
    • cluster indices over time can be found in clustered.tar.gz

  • Computation of Cross-Correlation between state and depth trajectory
    • to compute cross-correlation (link) median of each trajectory was substracted first, additonally the depth coordinate was inverted
    • cross-correlation was computed for possible time shifts from 0 to 250 steps in both directions
    • the resulting correlation values are depicted in the third plot, the maximal values is given in the title of it (remark: y axis should be named cross-correlation instead of auto-correlation)

Calculation of Electrostatic Potential

  • steps
    • removal of water and ions except MG-Ion (VMD selection: 'all and not water and not resname POT and not resname CLA and not resname SOD')
    • rename residue of first 6 atoms in PDB file to ACE, change ID to 0
    • do the same thing in PSF file
    • remove ATOMS 1046, 1047, 1048 from PDB and PQR
    • replace 1045 with HE2 in PDB and PSF PSF-PLOT '1045 ACTI 72 HSE HE2 H 0.000000 1.0080 0'
    • RUN pdb2pqr by: ~/progs/pdb2pqr-1.2.1/pdb2pqr.py --apbs-input --ff=charmm --ffout=charmm PDB_FILE TARGET_PQR
    • change 5785 - 5787 RESNAME to PHE in PQR-File
    • RUN replacement script: ../../scripts/assignCorrectChargesToPQR.pl actin_namd.psf actin_namd_clean.pqr actin_namd_repl.pqr


Analysed Simulation Data


Topic revision: r9 - 15 Jun 2012, AntoniaMey
 
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