Molecular Dynamics Simulations

Preparation

• repairPDB 1a6z.pdb -ssw 15t >ssw.tmp but there was no crystal water included.
• repairPDB 1a6z.pdb -nosol >1a6z_clean.pdb
• scwrl -i 1a6z_clean.pdb -s 1a6z_low.txt -o 1a6z_clean_complete.pdb > out.log
• 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