Difference between revisions of "Normal Mode Analysis BCKDHA"

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(References)
(NOMAD-Ref)
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== NOMAD-Ref ==
 
== NOMAD-Ref ==
   
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The NOMAD <ref>[[http://lorentz.dynstr.pasteur.fr/nma/submission.php]]</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?
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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==
 
==All-atom NMA using Gromacs on the NOMAD-Ref server==

Revision as of 13:25, 14 July 2011

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