Difference between revisions of "Structure-based mutation analysis BCKDHA"

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(4.pdb2gmx)
(6.grompp)
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===6.grompp===
 
===6.grompp===
 
grompp -v -f MDP_bckdha.mdp -c bckdha.gro -p topol.top -o bckdha.tpr
 
grompp -v -f MDP_bckdha.mdp -c bckdha.gro -p topol.top -o bckdha.tpr
 
 
 
processing coordinates...
 
double-checking input for internal consistency...
 
Reading position restraint coords from bckdha.gro
 
renumbering atomtypes...
 
 
GB parameter(s) missing or negative for atom type 'OW'
 
 
GB parameter(s) missing or negative for atom type 'HW'
 
 
-------------------------------------------------------
 
Program grompp, VERSION 4.5.3
 
Source code file: /build/buildd/gromacs-4.5.3/src/kernel/grompp.c, line: 1123
 
 
Fatal error:
 
Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for 2 atomtypes or they might be negative.
 
For more information and tips for troubleshooting, please check the GROMACS
 
website at http://www.gromacs.org/Documentation/Errors
 
-------------------------------------------------------
 
   
 
===7.System Minimization ===
 
===7.System Minimization ===

Revision as of 11:09, 30 June 2011

Structure selection

The following table presents the PDB structures for BCKDHA to date:

PDB id resolution [Å] R-factor coverage ph-value
1DTW 2.70 0.224 7.5*
1OLS 1.85 0.172 5.5
1OLU 1.90 0.161 5.5
1OLX 2.25 0.161 5.5
1U5B 1.83 0.156 5.8
1V11 1.95 0.139* 5.5
1V16 1.90 0.132* 5.5
1V1M 2.00 0.130* 5.5
1V1R 1.80 0.158 5.5
1WCI 1.84 0.149 5.5
1X7W 1.73 0.148 5.8
1X7X 2.10 0.149 5.8
1X7Y 1.57 0.150 5.8
1X7Z 1.72 0.154 5.8
1X80 2.00 0.161 5.8
2BEU 1.89 0.171 5.5
2BEV 1.80 0.139 5.5
2BEW 1.79 0.147 5.5
2BFB 1.77 0.145 5.5
2BFC 1.64 0.144 5.5
2BFD 1.39* 0.150 5.5
2BFE 1.69 0.150 5.5
2BFF 1.46 0.150 5.5
2J9F 1.88 0.171 5.5

The following PDB Structure was chosen because of its good experimental resolution: <bold></bold>

  • resultion:
  • R-factor
  • ph-value

Comparison energies

Mapping of the mutations on the crystal structure

SCWRL

Before we could use SCWRL we first had to get the sequence of our model: repairPDB bckdha.pdb -seq >> bckdha.seq

When we have the sequence we have to make one file for each mutation. In these files we copied the bckdha.seq and changed the sequence to lower case letters. Then we add the mutation in an upper case letter.

To run SCWRL we used the command: scwrl -i bckdha.pdb -s mutation1.seq -o mutation1Model.pdb


Total minimal energy of the graph

Position Energy
M82L 642.213
Q125E 616.85
Y166N 616.293
G249S 633.378
C264W 805.257
R265W 710.647
I326T 619.424
F409C 617.305
Y438N 615.951

foldX

To use foldX we first build a runscript. Additionally we had to create one file with all PDB Ids each in a new line (list.txt).


<TITLE>FOLDX_runscript;
<JOBSTART>#;
<PDBS>#;
<BATCH>foldx_protein.txt;
<COMMANDS>FOLDX_commandfile;
<Stability>list.txt;
<END>#;
<OPTIONS>FOLDX_optionfile;
//<Temperature>298;
<R>#;
<pH>5.5;
<IonStrength>0.050;
<water>-CRYSTAL;
<metal>-CRYSTAL;
<VdWDesign>2;
<OutPDB>false;
<pdb_hydrogens>false;
<END>#;
<JOBEND>#;
<ENDFILE>#;


total energy difference
wildtype 401.00 0
mutant1 437.88 -36.88
mutant2 431.77 -30.77
mutant3 432.24 -31.24
mutant4 432.22 -31.22
mutant5 488.43 -87.43
mutant6 460.43 -59.43
mutant7 432.94 -31.94
mutant8 433.33 -32.33
mutant9 431.56 -30.56

gromacs

Gromacs

1. fetchpdb

The fetch-pdb script first checks, if it was called with an valid PDB-id. If the entered PDB code has 4letters, the script tries to download the pdb-file from the server. The successfully downloaded folder gets unzipped and everything except the actual pdb file is removed.

2. repairPDB

3. SCWRL

scwrl -i bckdha_mod.pdb -s extractedPDB.seq -o bckdha_scwrl.pdb

pdb including HEATOMS

4.pdb2gmx

5. MDP

6.grompp

grompp -v -f MDP_bckdha.mdp -c bckdha.gro -p topol.top -o bckdha.tpr

7.System Minimization

8.Analyzation

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go back to Task 6 Sequence based mutation analysis

go to Reference Sequence BCKDHA