Team:EPF-Lausanne/Analysis

From 2009.igem.org

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(RMSD for individual residues)
(RMSD for individual residues)
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<b>4.</b> In VMD, in Graphics → Representations, do the following actions:  
<b>4.</b> In VMD, in Graphics → Representations, do the following actions:  
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; create two replicates: protein and resname FMN in selected atoms
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<ul>
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; for the FMN, choose CPK as a drawing method
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<li> create two replicates: protein and resname FMN in selected atoms
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<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; for the protein, choose tube as drawing method, and <i>user</i> as coloring method. Now click on the Trajectory tab, and in the Color Scale Data Range, type 0.40 and 1.00.
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<li> for the FMN, choose CPK as a drawing method
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<li> for the protein, choose tube as drawing method, and <i>user</i> as coloring method. Now click on the Trajectory tab, and in the Color Scale Data Range, type 0.40 and 1.00.
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[[Image:Vmd_color.png|200px|center]]
[[Image:Vmd_color.png|200px|center]]

Revision as of 11:45, 8 September 2009


Analysis of Equilibrium





Scripts

As this page is getting crowded, we created another page to explain all the scripts we wrote. The current page has some kind of step by step tutorials, but if you want fast informations, you better go to the script page.


Examples

Maxwell-Boltzmann Energy Distribution

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Energies

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Temperature distribution

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Density

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Pressure as a function of simulation time

Click here to show/hide

RMSD for individual residues

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RMSD of selected atoms compared to initial position along time

This script was highly updated, please go to the script page if you encounter a problem!!!

Selections are not precise here!


We made a small TCL script to calculate RMSD from selected atoms compared to their initial position along timestep. The file can be found here. Please rename to Residue_rmsd_igem09.tcl after download.

Example to run the script:

load .dcd + .psf on VMD
source residue_rmsd_igem09.tcl
set sel_resid [[atomselect top "protein and alpha"] get resid]
rmsd_residue_over_time top $sel_resid 0 0

We tried to select only backbone from protein + FMN → change

set sel_resid [[atomselect top "backbone"] get resid]

The script was updated to be able to define reference frame and first frame were RMSD will be calculated. We usually don't need to compute RMSD during heating, for instance. RMSD takes a lot of time. In our first run 1 frame = 100 timesteps * 2 fs*timesteps^-1 = 200 fs

complete form for run is:

rmsd_residue_over_time top $sel_resid FIRST_FRAME REFERENCE_FRAME

For our first run, if we want to select only the 295°K NPT plateau, and set its first frame as reference, we have to launch:

rmsd_residue_over_time top $sel_resid 1115 1115

Here is how the script processes:

  • calculate how many frames are in .dcd
  • for each timestep, the script aligns (best fit) the backbone of the protein to the eference position to minimize RMDS. (Test: "and not mass 1,008000" == and noh was added in selection to remove hydrogen)
  • for each residue (selected by sel_resid), RMSD is computed and the sum of all RMSD (one for each residue) is stored for current timestep
  • script's output is data_rmsd.dat


Here is a fast graph of the output of the average RMSD of the atoms in function of time. It seems normal.

Rmsd.jpg


Here is what we got with FIRST_FRAME=1115 REFERENCE_FRAME=1115. Average=921.477, standard deviation=202.1708

RMSD plateau.jpg


FIRST_FRAME=0 REFERENCE_FRAME=0. The difference of the sum probably comes from the new selection of atoms from the backbone. We should compute an average value to normalize amplitude. (fluctuation is conserved, anyway) Average=781.3913, standard deviation=118.1393

RMSD COMPLETE RUN.jpg



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Salt bridges

As we wanted to redo the analysis from Schulten's article, we looked for salt bridges. VMD can easily compute this, it even propose an easy GUI. Standard configuration is just fine for now. You'll have a log file containing the list of nitrogen-oxygen susceptible of forming a salt bridge. You'll also get a file for each bridge containing the distance between both atoms along the simulation.

In the light state, we have 9 salt bridges witin the protein and 12 if we consider the protein and the flavin (use "protein or resname FMN" as selection).

ASP471-ARG467
GLU409-ARG442
FMN450-FMN450
ASP540-LYS544
ASP432-ARG442
FMN450-ARG451
GLU457-LYS489
GLU444-LYS485
ASP522-ARG521
ASP424-ARG451
GLU475-LYS533
FMN450-ARG467

Here is a plot for one of the bridges. We have to look for the max distance for a salt bridge.

Salt bridge.jpg


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RMSF

After changing the script [see here], we perform an interesting analysis from these 2 files. First, we have to correct the RMSF, that can be linked to beta factor using this equation:

Beta rmsf.jpg

If you plot beta factor and RMSF, you get such a thing. center‎

This is a 1 nanosecond NPT run at 300°K. We hope to see a RMSF curve identical to the beta factor. It should only be shifted higher because of the increased temperature. But having a similar tendency would mean our simulation show oscillations similar to what was observed during crystallography. This is really a quite nice validation of our run!


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