Normal Mode Analysis BCKDHA

From Bioinformatikpedia
Revision as of 13:36, 14 July 2011 by Demel (talk | contribs) (NOMAD-Ref)

WEBnm@

ElNemo

Anisotropic Network Model web server

oGNM – Gaussian network model

NOMAD-Ref

The NOMAD <ref>[[1]]</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
All distances are weightend by this parameter which introduced a smoother cutoff value that in the original Tirion model. 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
    • 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