Normal Mode Analysis BCKDHA
From Bioinformatikpedia
Contents
WEBnm@
ElNemo
Anisotropic Network Model web server
oGNM – Gaussian network model
NOMAD-Ref
The NOMAD <ref>[[1]]</ref> server does provide a lot of information. The following parameters can be set:
- Number of modes to calculate
- Distance weight parameter
- Cutoff to use for mode calculation
- Average Rmsd in output trajectories
- Method to use
- Automatic
- Full matrix solver
- Sparse matrix solver
- Here we used the default option, the automatic mode.
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”…
All-atom NMA using Gromacs on the NOMAD-Ref server
In order to do the all-atom NMA we needed to prepare our PDB file. The PDB file for 1BPT protein contains 1629 atoms in total, all lines not beginning with "ATOM" were removed from the PDB file.
Advantages and Disadvantages from NMA and MD
References
<references />
go back to Task 8: Molecular Dynamics Simulations