Difference between revisions of "Molecular Dynamics Simulations BCKDHA"

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(Preparation)
(Preparation)
Line 10: Line 10:
 
: 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.
 
: 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.
 
; Extract Protein
 
; Extract Protein
  +
: <code>repairPDB bckdha_mod -nosol >wt.pdb</code>
  +
; SCWRL
 
: first, extract sequence from pdb file:
 
: first, extract sequence from pdb file:
 
: <code> repairPDB bckdha_mod.pdb -seq > wt.seq </code>
 
: <code> repairPDB bckdha_mod.pdb -seq > wt.seq </code>
 
: run SCWRL
 
: run SCWRL
: <code>repairPDB bckdha_mod -nosol >wt.pdb</code>
+
: <code>scwrl -i wt.pdb -s wt.seq -o wt.pdb</code>
; SCWRL
 
: <code>scwrl -i wt.pdb -s wt.seq
 
 
: wt.seq is the extracted protein sequence in all lower case letters. In the case of mutants the mutated residue is given in an upper case letter.
 
: wt.seq is the extracted protein sequence in all lower case letters. In the case of mutants the mutated residue is given in an upper case letter.
  +
; remove hydrogens
 
use repairPDB and extract just protein. <-nosol>
+
: <code> repairPDB wt.pdb -noh > wt.pdb
  +
; Concatenate protein and crystal water
now use SCWRL with the extracted protein and give it the PDB sequence in all small letter to complete missing sidechains
 
  +
: As we didn't have crystal water, the concatenation step could be skipped.
remove the hydrogen atoms from the SCWRL output with repairPDB
 
concatenate the protein and the crystal water into one file
 

Revision as of 17:32, 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.pdb
bckdha_mod.pdb is the manipulated pdb from last tast, where the missing residues in the 1U5B pdb file were handled.
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.
Extract Protein
repairPDB bckdha_mod -nosol >wt.pdb
SCWRL
first, extract sequence from pdb file:
repairPDB bckdha_mod.pdb -seq > wt.seq
run SCWRL
scwrl -i wt.pdb -s wt.seq -o wt.pdb
wt.seq is the extracted protein sequence in all lower case letters. In the case of mutants the mutated residue is given in an upper case letter.
remove hydrogens
repairPDB wt.pdb -noh > wt.pdb
Concatenate protein and crystal water
As we didn't have crystal water, the concatenation step could be skipped.