Protocol BCKDHA MD

A brief check of results

To verified that the simulations finished properly we first use the command

• gmxcheck -f wt.xtc

Quality assurance

Energy calculations

To calculate the different energies we used the command:
g_energy -f wtMD.edr -o energy.xvg
After submitting this command we had to choose the energy which should calculated.

• Pressure: 13
• Temperature: 12
• Potential: 9
• Total Energy: 11

Minimum distance between periodic boundary cells

It is important to calculate the minimal distances to find out if there are direct interactions. Such interactions could appear if the distances are shorter than the cut off value of electrostatic interactions.

To calculate the minimum distance we used the command
g_mindist -f wtMD.xtc -s wtMD.tpr -od minimal-periodic-distance.xvg -pi
After submitting this command we chose group 1 to calculate the minimum distance for the whole protein.

Root mean square fluctuations

For calculating the RMSF of a protein each atom of this protein is compared with the calculated average stucture of the protein. By comparing them it is possible to find out how much it varies from its average position and so the flexibility of this region can be calculated. Regions with a high fluctuation are more flexible than regions with a low one.

To calculate the minimum distance we used the command
g_rmsf -f wtMD.xtc -s wtMD.tpr -o rmsf-per-residue.xvg -ox average.pdb -oq bfactors.pdb -res
After submitting this command we had to choose the group we want the RMSF to be calculated for:

• Protein: 1
• C-alpha: 3

Radius of gyration

The radius of gyration reflects how the structure changes during the simulation and how the shape changes during the time.

To calculate the radius of gyration we used the command
g_gyrate -f wtMD.xtc -s wtMD.tpr -o radius-of-gyration.xvg
After submitting this command we chose group 1 to calculate the radius of gyration for the whole protein

Structural analysis

First we had to use the command
trjconv -f wtMD.xtc -o wtMD_nojump.xtc -pbc nojump
This is important because the protein possibly jumps out of the box so the trajectory has to be rebuild. This has the effect that the particles are back in the center.

Solvent accessible surface area

The solvent accessible surface area (SASA) of a protein is the part of the surface which is reachable a solvent. This definition of SASA can be devided into two subgroups - hydrophilic SASA and hydrophobic SASA. Which means that the possibility that a solvent can reach the surface depends on its properties.

To calculate the solvent accessible surface area we used the command
g_sas -f wtMD_nojump.xtc -s wtMD.tpr -o solvent-accessible-surface.xvg -oa atomic-sas.xvg -or residue-sas.xvg
After submitting this command we had to choose two groups. Both times we chose protein.