Molecular Dynamics Simulations

Preparation

• We extracted all crystal water but, there was no crystal water included.
  • cmd: repairPDB 1a6z.pdb -ssw 15t >ssw.tmp
• Extracting the pure protein
  • cmd: repairPDB 1a6z.pdb -nosol >1a6z_clean.pdb
• Complete missing side chains
  • cmd: scwrl -i 1a6z_clean.pdb -s 1a6z_low.txt -o 1a6z_clean_complete.pdb > out.log
• Removing all H-Atoms
  • cmd: 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

• cmd: 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
  • cmd: editconf -f 1a6z_final.gro -o 1a6z_final_box.gro -bt dodecahedron -d 1.0
    
• The box was afterwards filled with water
  • cmd: 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
  • cmd: grompp -v -f first.mdp -c 1a6z_final_box_water.gro -p 1a6z_final.top -o 1a6z_final_box_water.tpr

Genion

• cmd: 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. 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.
  • cmd: tr -s ' ' '\n' < out.txt | grep -c 'ION'

• Next we 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.

• After adding the new water, we checked for an overlap with the crystal water but as we had no crystal water in our file, we assumed to have no overlap. And as we found no REMARK tag in the new file, we should have no overlap
  • cmd: repairPDB 1a6z_solv.pdb -cleansol > 1a6z_solv2.pdb

• In this step we added restrains to disable very fast vibrations such as seen for hydrogen atoms to reduce the simulation time.
  • cmd: genrestr -f 1a6z_solv2.pdb -o 1a6z.itp

Minimization solvent and system

• We first created a new .tpr file.
  • cmd: grompp -v -f second.mdp -c 1a6z_solv.pdb -p 1a6z_final_ion.top -o 1a6z_solv_min.tpr
• But if we used the pdb-file created with the last repairPDB call which should check for overlaping water, we get an error which tells us that the number of coordinates in the pdb file does not match the number of coordinates in the top-file. Therefore we used the pdb-file which was not "repaired".
• Afterwards we minimised the solvent.
  • cmd: mpirun -np 4 mdrun_mpi -v -deffnm 1a6z_solv_min.tpr -c 1a6z_solv_min.pdb.
• To minimise the solvent and the protein sidechains and to create a new .tpr file.
  • cmd: genrestr -f 1a6z_solv_min.pdb -o 1a6z_min.itp
• To prepare a new .tpr file.
  • cmd: grompp -v -f second.mdp -c 1a6z_solv_min.pdb -p 1a6z_final_ion.top -o 1a6z_solv_min2.tpr
• At last we minimised the total system
  • cmd: mpirun -np 4 mdrun_mpi -v -deffnm 1a6z_solv_min2.tpr -c 1a6z_solv_min2.pdb

Equilibration of system

• First we created a new .tpr file using grompp -v -f nvt.mdp -c 1a6z_solv_min2.pdb -p 1a6z_final_ion.top -o 1a6z_nvt.tpr and then started rhe mdrun with mpirun -np 4 mdrun_mpi -v -deffnm 1a6z_nvt.tpr -c 1a6z_nvt.pdb.
• The second step was to create a new .tpr file for pressure coupling by grompp -v -f <npt.mdp> -c <file_nvt.gro> -p <file.top> -o <file_npt.tpr>. But to get an adepted .gro file, we had to use pdb2gmx a second time with pdb2gmx -f <input.pdb> -o <output.gro> -p <output.top> -water tip3p -ff amber03 -vsite hydrogens. For startinf the mdrun we used again the command mpirun -np 4 mdrun_mpi -v -deffnm 1a6z_nvt.tpr -c 1a6z_nvt.pdb

Production run

• grompp -v -f <md.mdp> -c <file_npt.gro> -p <file.top> -o <file_md.tpr>. To get the new .gro file we again used pdb2gmx.