Normal Mode Analysis BCKDHA
Anisotropic Network Model web server
oGNM – Gaussian network model
The NOMAD <ref>[]</ref> server provides a lot of information and options. The interface is quite user friendly as all available parameter choices are explained in detail and there is also the runtime listed for an example NMA, which can be used to estimate the runtime for our own jobs.
The following parameters can be set:
- Number of modes to calculate
- As specified in the task description we wanted to obtain 10 modes. NOMAD does six zero modes which are just translation and rotation. Therefore we set the number of modes to calculate to 16.
- Distance weight parameter
- This parameter is used to introduce a smoother cutoff value that in the original Tirion model. All distances are weightend by exp(-(d_ij/d)^2), where d is the distance weight parameter. As proposed by NOMAD a distance weight parameter of 3Å is well suited for CA-only models. As we are doing no all-atom calculation, the distance weight parameter was set to 3.0Å.
- Cutoff to use for mode calculation
- The cutoff describes which pairs of atomes are linked by a spring of universal length according to the Tirion model (Elastic Network Model). The cutoff was set to 15Å.
- Average Rmsd in output trajectories
- For the average RMSD the default value (3.0) was used.
- Method to use
- Full matrix solver
- Sparse matrix solver
- Here we used the default option, the automatic mode.
The output contains one PDB file and one plot per mode. The plot contains the rmsd per residue, which can be interpreted as the amplitude of movement and which is controlled by the average rmsd of trajectory (input parameter).
What information do the different servers provide? Which regions of your protein are most flexible, most stable? When you visualize the modes (provided by server or using for example PyMol or VMD), try to describe what movements you observe? Hinge-movement, “breathing”…
|mode 1||mode 2||mode 3||mode 4||mode 5|
All-atom NMA using Gromacs on the NOMAD-Ref server
In order to do the all-atom NMA we needed an appropriate small molecule that contained not more than 2000 atoms. This small protien was found by searching for "all atom nma". We found a paper <ref>Hetunandan Kamisetty, Eric P. Xing and Christopher J. Langmead: Free Energy Estimates of All-atom Protein Structures Using Generalized Belief Propagation[]</ref>. They used the structure of a hen egg-white lysozyme for an all atom NMA. So we did all the calculations for the corresponding PDB entry 2lyz.
First, we needed to prepare our PDB file. The PDB file for 2LYZ protein contains 1001 atoms in total, all lines not beginning with "ATOM" were removed from the PDB file.
The following movies show the all-atom NMA for 2LYZ at 200K
|mode 1||mode 2||mode 3|
The following movies show the all-atom NMA for 2LYZ at 600K
|mode 1||mode 2||mode 3|
Advantages and Disadvantages from NMA and MD
go back to Task 8: Molecular Dynamics Simulations