Coarse grained simulation of Rab5a

• Isolated the Rab5a from GppNHp by doing the steps below:
• cp 1n6h.pdb 1n6h_clean.pdb
• grep GNP 1n6h_clean.pdb > GNP.pdb

For example: “HETATM”

• grep -v "HETATM" 1n6h_clean.pdb > AA.pdb

Made AA.pdb that did not include “HETATM”

1n6h_clean.pdb was renamed 1n6h_dirty.pdb

removed 1n6h_clean.pdb

AA.pdb was renamed 1n6h_clean.pdb

removed AA.pdb

• gmx pdb2gmx -f 1n6h_clean.pdb -o 1n6h_processed.gro -water spc

Picked 9: GROMOS96 43a1 force field

• python martinize.py -f 1n6h_processed.gro -o single-ubq.top -x 1n6h_processed-CG.pdb -p backbone -ff martini22
• gmx editconf -f 1n6h_processed-CG.pdb -d 1.0 -bt cubic -o 1n6h_processed-CG.gro
• gmx grompp -p single-ubq.top -f minimization.mdp -c 1n6h_processed-CG.gro -o minimization-vac.tpr
• gmx mdrun -deffnm minimization-vac -v
• gmx solvate -cp minimization-vac.gro -cs water.gro -radius 0.21 -o solvated.gro
• gmx grompp -p system.top -c solvated.gro -f minimization.mdp -o minimization.tpr

You’re going to get an error but make sure to match the number of coordinates for solvated.gro and system.top and then run this command again

• gmx mdrun -deffnm minimization -v
• gmx grompp -p system.top -c minimization.gro -f equilibration.mdp -o equilibration.tpr
• gmx mdrun -deffnm equilibration -v
• gmx grompp -p system.top -c equilibration.gro -f dynamic.mdp -o dynamic.tpr -maxwarn 1
• gmx mdrun -deffnm dynamic -v
• gmx trjconv -f dynamic.xtc -s dynamic.tpr -fit rot+trans -o viz.xtc

Picked 1: Protein

Picked 0: System

• vmd equilibration.gro viz.xtc
• gmx trjconv -f dynamic.xtc -s dynamic.tpr -fit rot+trans -o * * viz.pdb -conect

Picked 1: Protein

Picked 0: System

• vmd viz.pdb