Molecular Dynamics Simulations Hemochromatosis

Hemochromatosis>>Task 8: Molecular dynamics simulations

Riddle of the task

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Short task description

Detailed description: Molecular dynamics simulations

Protocol

A protocol with a description of the data acquisition and other scripts used for this task is available here.

Diary of "trial and error"-hell...

Tipps for other groups:

• AGroS wants to run "scwrl" and not "Scwrl4" which is the name after the installation.
  • Solution: ln -s Scwrl4 scwrl

• Problems NVT!!! (Can not open file: *_nvt.tpr).
  • Solution: reduce to 16 cores (instead of 32)
    • Anybody tried 32 cores on the real runs??
      • Yes, tried and it worked in the real run. The --partition=inter queue still throws segfaults on the NVT run, though.. ;)

Current "test" state:

• Run min I: solvent & fixed protein(SD) ...finished
• Run min II: solvent & fixed backbone(SD) ...finished
• Run min III: solvent & fixed backbone(CG) ...finished
• Run NVT ...finished
• Run NPT ...finished
• Production run ...terminated after the 2 hour limit (without errors)

Starting mutation runs:

• Wildtype (status: finished...)
• R224W (status: running...)
• C282S (status: running...)

AGroS pipeline and intermediate PDB files

The different steps performed by AGroS:

• Runs RepairPDB and findBreaks, additional scripts to adapt PDB files to MD reality.
• Runs STRWater, an additional script that saves information for Structural Water Molecules in PDB file.
• Runs SCWRL, a program employed to correctly assign side chain information to PDB structures.
• Runs minimization in vacuum.
• Creates water box, includes solvent (water with 0.1 [NaCl]) and neutralizes protein intrinsic charge.
• Creates restrain files for each chain individually.
• Runs solvent minimization with fixed Protein (backbone + sidechains).
• Runs minimization with fixed Backbone.
• Runs minimization with fixed Backbone (CG).
• Runs short production NVT MD.
• Runs short production NPT MD.
• Runs Production MD.

Intermediate PDB files:

• 1a6zC.pdb (clashing water removed)
• 1a6zC_br.pdb (just the protein to find breaks)
• 1a6zC_br_0.pdb (same as above, but one file per chain)
• 1a6zC.pdb2 (hydrogens removed)
• 1a6zC_repair.pdb (without DNA and renumbered residues)
• 1a6zC_repair_0.pdb (same as above, but one file per chain)
• 1a6zC_water.pdb (structural water, B-Factor cutoff 15)
• 1a6zC_dna.pdb (just the DNA)
• 1a6zC_sc.pdb (SCWRL output for 1a6zC_repair.pdb)
• 1a6zC_nh.pdb (protein, plus structural water, plus DNA)
• 1a6zC_solv_tmp.pdb (ions added)
• 1a6zC_solv.pdb (duplicate water removed)
• 1a6zC_solv.pdb2 (protein, plus DNA)
• 1a6zC_solv_0.pdb (input to generate restrictions per chain)
• 1a6zC_solv_min.pdb (minimized solvent with fixed protein)
• 1a6zC_solv_min.pdb2 (just the protein)
• 1a6zC_solv_min_0.pdb (input to generate restrictions per chain)
• 1a6zC_solv_min2.pdb (minimization with fixed backbone)
• 1a6zC_solv_min3.pdb (minimization with fixed backbone, with conjugate gradient)