Difference between revisions of "MD Mutation436"
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|colspan="3" | Perspective two |
|colspan="3" | Perspective two |
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| − | | [[Image: |
+ | | [[Image:average_original_c_2.png|thumb|Alignment of the original structure (green) and the calculated average structure of the c-alpha atoms (turquoise)]] |
| − | | [[Image: |
+ | | [[Image:bfactor_original_c_2.png|thumb|Alignment of the original structure (green) and the calculated structure with high B-Factor values of the c-alpha atoms (turquoise)]] |
| − | | [[Image: |
+ | | [[Image:bfactor_average_c_2.png|thumb| Alignment of the structure with high B-Factor values of the c-alpha atoms (red) and the calculated average structure of the c-alpha atoms (blue)]] |
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|colspan="3" | RMSD |
|colspan="3" | RMSD |
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As in the section above, the RMSD between the structure with high B-factor values and the original structure is the most similar. This was expected, because we used twice the same model, but in this case we neglecte the residues of the atoms. But the backbone of the protein remains the same. |
As in the section above, the RMSD between the structure with high B-factor values and the original structure is the most similar. This was expected, because we used twice the same model, but in this case we neglecte the residues of the atoms. But the backbone of the protein remains the same. |
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| + | |||
| + | Furthermore, we got a plot of the RMSF values of the protein, which can be seen in the following plot: |
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| + | |||
| + | [[Image:bfactor_plot_calpha.png|thumb|center|Distribution of the b-factor values by only regarding the backbone of the protein.]] |
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| + | |||
| + | In this case, there is only one high peak at position 150. By observing the whole protein, it was possible to see, that the position of the beta sheet differs extremely between the two models. The other peak at position 440 could not be found in the plot. By a look at the picture above, we can see that the backbone do not differ extremely between the two models. Therefore, in this case the position of the residues has to be very different, which is not important in our case, because we do not regard side chains. |
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=== Pymol analysis of average and bfactor === |
=== Pymol analysis of average and bfactor === |
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Revision as of 14:31, 29 August 2011
Contents
- 1 check the trajectory
- 2 Visualize in pymol
- 3 create a movie
- 4 energy calculations for pressure, temperature, potential and total energy
- 5 minimum distance between periodic boundary cells
- 6 RMSF for protein and C-alpha
- 7 Pymol analysis of average and bfactor
- 8 Radius of gyration
- 9 solvent accesible surface area
- 10 hydrogen-bonds
- 11 salt bridges
- 12 Ramachandran plot
- 13 RMSD matrix
- 14 cluster analysis
- 15 internal RMSD
check the trajectory
We checked the trajectory with following command:
gmxcheck -f mut436_md.xtc
With the command we got following results:
Reading frame 0 time 0.000 # Atoms 96555 Precision 0.001 (nm) Last frame 2000 time 10000.000
Furthermore, we got some detailed results about the different items during the simulation.
| Item | #frames | Timestep (ps) |
| Step | 2001 | 5 |
| Time | 2001 | 5 |
| Lambda | 0 | - |
| Coords | 2001 | 5 |
| Velocities | 0 | - |
| Forces | 0 | - |
| Box | 2001 | 5 |
The simulation finished on node 0 Fri Aug 26 08:40:07 2011.
| Time | ||
| Node (s) | Real (s) | % |
| 34860.474 | 34860.474 | 100% |
| 9h41:00 | ||
The complete simulation needs 9 hours and 41 minutes to finishing.
| Performance | |||
| Mnbf/s | GFlops | ns/day | hour/ns |
| 818.560 | 60.105 | 24.785 | 0.968 |
As you can see in the table above, it takes about 1 hour to simulat 1ns of the system. So therefore, it would be possible to simulate about 25ns in one complete day calculation time.
Visualize in pymol
First of all, we visualized the simulation with with ngmx, because it draws bonds based on the topology file. ngmx gave the user the possibility to choose different parameters. Therefore, we decided to visualize the system with following parameters:
| Group 1 | Group 2 |
| System | Water |
| Protein | Ion |
| Backbone | NA |
| MainChain+H | CL |
| SideChain |
Here is a picture of the visualization with ngmx:
Next, we want to visualize the protein with pymol. Therefore, we extracted 1000 frames from the trajectory, leaving out the water and jump over the boundaries to make continuse trajectories. Therefore, we used following command:
trjconv -s fole.tpr -f file.xtc -o output_file.pdb -pbc nojump -dt 10
The program asks for the a group as output. We want to see the whole system, therefore we decided to use group 0.
create a movie
energy calculations for pressure, temperature, potential and total energy
Temperature
| Average (in K) | 297.94 |
| Error Estimation | 0.0029 |
| RMSD | 0.944618 |
| Tot-Drift | 0.00834573 |
The plot with the temperature distribution of the system can be seen here:
Potential
| Average (in kJ/mol) | -1.28165e+06 |
| Error Estimation | 100 |
| RMSD | 1080.9 |
| Tot-Drift | -714.814 |
The plot with the potential energy distribution of the system can be seen here:
Total energy
| Average (in kJ/mol) | -1.0519e+06 |
| Error Estimation | 100 |
| RMSD | 1322.68 |
| Tot-Drift | -708.38 |
The plot with the total energy distribution of the system can be seen here:
Pressure
| Average (in bar) | 1.0066 |
| Error Estimation | 0.014 |
| RMSD | 71.218 |
| Tot-Drift |
The plot with the pressure distribution of the system can be seen here:
minimum distance between periodic boundary cells
Next we try to calculate the minimum distance between periodic boundary cells. As before, the program asks for one group to use for the calculation and we decided to use only the protein, because the calculation needs a lot of time and the whole system is significant bigger than only the protein. So therefore, we used group 1.
RMSF for protein and C-alpha
Protein
First of all, we calculate the RMSF for the whole protein.
The analysis produce two different pdb files, one file with the average structure of the protein and one file with high B-Factor values, which means that the high flexbile regions of the protein are not in accordance with the original PDB file.
To compare the structure we align them with pymol with the original structure.
| original & average | original & B-Factors | average & B-Factors |
| Perspective one | ||
| Perspective two | ||
| RMSD | ||
| 1.525 | 0.348 | 1.671 |
The structure with the high B-factors is the most similar structure compared with the original structure from PDB. The average structure is not that similar. But we know, that the regions with high B-Factors are very flexible, and therefore in the structure downloaded from the PDB, the protein is in another state, because of its flexible regions. Therefore, because of the low RMSD between the high B-factors structure and the original structure we can see, that the simulation predicts the structure quite good.
Furthermore, we got a plot of the RMSF values of the protein, which can be seen in the following plot:
There are two regions with very high B-factor values. One region at position 150, and the other region at position 440. If we compare the picture of the original and the average structure, we can see that most of the regions build a very good alignment, whereas some regions vary in their position. Therefore, we want to compare, if these regions are the regions with very high B-factor values.
As you can see in the pictures above, especially in the first picture, which is the part with the highest peak in the plot, the structures have a very different position and the alignment in this part of the protein is very bad, although the rest of the alignment is quite good. This also explains the relatively high RMSD values, because of the different positions of the flexible parts of the protein.
C-alpha
Now we repeat the analysis done for the protein for the C-alpha atoms of the protein. Therefore, we followed the same steps as in the section above.
To compare the structure we align them with pymol with the original structure.
| original & average | original & B-Factors | average & B-Factors | |||
| Perspective one | |||||
| Perspective two | |||||
| RMSD | 1.324 | 0.277 | 1.334 | ||
As in the section above, the RMSD between the structure with high B-factor values and the original structure is the most similar. This was expected, because we used twice the same model, but in this case we neglecte the residues of the atoms. But the backbone of the protein remains the same.
Furthermore, we got a plot of the RMSF values of the protein, which can be seen in the following plot:
In this case, there is only one high peak at position 150. By observing the whole protein, it was possible to see, that the position of the beta sheet differs extremely between the two models. The other peak at position 440 could not be found in the plot. By a look at the picture above, we can see that the backbone do not differ extremely between the two models. Therefore, in this case the position of the residues has to be very different, which is not important in our case, because we do not regard side chains.
