Difference between revisions of "Molecular Dynamics Simulations BCKDHA"

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(Created page with "== Preparation == For the molecular dynamics simulation two mutations should be chosen. We decided to take one mutation, which leads to a drastic change in the amino acid proper…")
 
(Preparation)
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For the molecular dynamics simulation two mutations should be chosen. We decided to take one mutation, which leads to a drastic change in the amino acid properties and may therefore be crucial. The other mutation changes methionine to lysine, which have similar physiochemical properties and structures. The mutations we chose are the following:
 
For the molecular dynamics simulation two mutations should be chosen. We decided to take one mutation, which leads to a drastic change in the amino acid properties and may therefore be crucial. The other mutation changes methionine to lysine, which have similar physiochemical properties and structures. The mutations we chose are the following:
* M82L: in PDB position 37
+
* M82L: (in PDB position 37)
*C264W: in PDB position 219
+
*C264W: (in PDB position 219)
  +
  +
; Crystal water Extraction
  +
: <code> repairPDB bckdha_mod.pdb -ssw 15 > crystalWater.pdb</code>When trying to extract the crystal water we received an empty file, indicating that there is no crystal water below 15 Å in our pdb file.
  +
  +
use repairPDB and extract just protein. <-nosol>
  +
now use SCWRL with the extracted protein and give it the PDB sequence in all small letter to complete missing sidechains
  +
remove the hydrogen atoms from the SCWRL output with repairPDB
  +
concatenate the protein and the crystal water into one file

Revision as of 17:07, 5 July 2011

Preparation

For the molecular dynamics simulation two mutations should be chosen. We decided to take one mutation, which leads to a drastic change in the amino acid properties and may therefore be crucial. The other mutation changes methionine to lysine, which have similar physiochemical properties and structures. The mutations we chose are the following:

  • M82L: (in PDB position 37)
  • C264W: (in PDB position 219)
Crystal water Extraction
repairPDB bckdha_mod.pdb -ssw 15 > crystalWater.pdbWhen trying to extract the crystal water we received an empty file, indicating that there is no crystal water below 15 Å in our pdb file.

use repairPDB and extract just protein. <-nosol> now use SCWRL with the extracted protein and give it the PDB sequence in all small letter to complete missing sidechains remove the hydrogen atoms from the SCWRL output with repairPDB concatenate the protein and the crystal water into one file