Molecular Dynamics Simulations

Preparation

• We extracted all crystal water by repairPDB 1a6z.pdb -ssw 15t >ssw.tmp but, there was no crystal water included.
• Extracting the pure protein by repairPDB 1a6z.pdb -nosol >1a6z_clean.pdb
• Complete missing side chains with scwrl -i 1a6z_clean.pdb -s 1a6z_low.txt -o 1a6z_clean_complete.pdb > out.log
• Remove all H-Atoms by repairPDB 1a6z_clean_complete.pdb -noh >1a6z_final.pdb
• because there was no crystal water in the origin pdb included, we had nothing to concatenate.

Creation of the gromac files

• pdb2gmx -f 1a6z_final.pdb -o 1a6z_final.gro -p 1a6z_final.top -water tip3p -ff amber03 -vsite hydrogens

Then a box around our protein was added by editconf -f 1a6z_final.gro -o 1a6z_final_box.gro -bt dodecahedron -d 1.0
and filled this box with water by using genbox -cp 1a6z_final_box.gro -cs spc216.gro -p 1a6z_final.top -o 1a6z_final_box_water.gro

Now we create the .tpr file for further use with genion by grompp -v -f first.mdp -c 1a6z_final_box_water.gro -p 1a6z_final.top -o 1a6z_final_box_water.tpr

Genion is udes with genion -s 1a6z_final_box_water.tpr -o 1a6z_solv.pdb -conc 0.1 -neutral -pname NA+ -nname CL- Now we counted the added ions by using tr -s ' ' '\n' < out.txt | grep -c 'ION'. ION is set to NA+ and CL- to get the number of added ions. For CL- genion added 41 and for NA+ genion added 52 ions.

• the Next step was to edit the SOL entry in the .top file. Here we found a SOL entry of 21363 which we changed to 21363-52-41=21270

and added two new entrys, NA with the value 52 and CL with the value 41.