Difference between revisions of "Molecular Dynamics Simulations BCKDHA"
From Bioinformatikpedia
(→Preparation) |
(→Preparation) |
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: 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. |
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; Extract Protein |
; Extract Protein |
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| + | : <code>repairPDB bckdha_mod -nosol >wt.pdb</code> |
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| + | ; SCWRL |
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: first, extract sequence from pdb file: |
: first, extract sequence from pdb file: |
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: <code> repairPDB bckdha_mod.pdb -seq > wt.seq </code> |
: <code> repairPDB bckdha_mod.pdb -seq > wt.seq </code> |
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: run SCWRL |
: run SCWRL |
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| − | : <code> |
+ | : <code>scwrl -i wt.pdb -s wt.seq -o wt.pdb</code> |
| − | ; SCWRL |
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| − | : <code>scwrl -i wt.pdb -s wt.seq |
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: 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. |
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| + | ; remove hydrogens |
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| − | |||
| − | + | : <code> repairPDB wt.pdb -noh > wt.pdb |
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| + | ; Concatenate protein and crystal water |
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| − | now use SCWRL with the extracted protein and give it the PDB sequence in all small letter to complete missing sidechains |
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| + | : As we didn't have crystal water, the concatenation step could be skipped. |
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| − | remove the hydrogen atoms from the SCWRL output with repairPDB |
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| − | concatenate the protein and the crystal water into one file |
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Revision as of 16:32, 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.
