Following is method to generate files required for protein hetero-atom complex
This tutorial assumes you have GROMACS 2018 installed and working in a directory with input PDB file named as bound_protein.pdb. Using this you will make your protein ligand complex system followed by Temperature - Pressure Equilibration and Final production run on 10 cores.
GROMACS-2018
Before we star we would like you to remove the ligand molecule from your PDB file using any of your prefered softwares (VMD/PYMOL); Please save the protein molecule as a new file named as protein.pdb before starting.
1. Converting PDB input to GROMACS compatible file.
gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce
# This first step will make topology file on the basis of your selected forcefield and your protein of interest also it generates an atomic cordinate file for the protein.
2. Generating atomic for the ligand molecule
gmx editconf -f bound_protein.pdb -o bound_protein.gro
3. Generating cordinates and other parameters for the ligand molecule
#For this step we will be using PRODRG server which will geerate .itp file for your ligand.
4. Incorporating the atomic cordinates of the ligand molecule into the protein.gro file
The atomic cordinates can directly be incorporated in the "protein_processed.gro" file just below the last atom and remember to increase the number of atom counts in this file (found in the first line of the gro) by the number of atoms added in the form of ligand. Do the incorporation and save the file as complex.gro
The .itp file generated using the PRODRG server has to saved as ligand.itp file in your working directory
Finally to tell the topol.top file about the incorporation of ligand you need to do the following
1. Add the following lines just after posre.itp reference at the bottom of topol.top
------------------------------------------------
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include ligand topology
#include "ligand.itp"
------------------------------------------------
2. Add the index of the ligand in the last line of the topol.top file (Replace the residue name of your ligand with XYZ)
Protein_chain_A 1
XYZ 1
2. Making a Box to make a boundary for box for simulation.
gmx editconf -f complex.gro -o protein_newbox.gro -c -d 1.0 -bt cubic
3. Adding water molecule to the system.
gmx solvate -cp protein_newbox.gro -cs spc216.gro -o protein_solv.gro -p topol.top
4. Generating .tpr file; get ions.mdp here
gmx grompp -f ions.mdp -c protein_solv.gro -p topol.top -o ions.tpr
5. Adding Ions to neutralised the system.
gmx genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1
6. Generating .tpr file; get minim.mdp here
gmx grompp -f minim.mdp -c protein_solv_ions.gro -p topol.top -o em.tpr
7. Running Energy Minimization to re-arrange ions.
gmx mdrun -v -deffnm em
# sucess of this energy minimization step tells you that you did a good job
8. Plotting Potential of the system.
gmx energy -f em.edr -o potential.xvg
9. Generating .tpr file; get nvt.mdp here
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
10. Running Temperature Equilibrating.
gmx mdrun -v -pin on -ntmpi 2 -ntomp 10 -deffnm nvt
11. Plotting Temperature of the system.
gmx energy -f nvt.edr -o temperature.xvg
12. Generating .tpr file; get npt.mdp here
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
13. Running Pressure Equilibrating.
gmx mdrun -v -pin on -ntmpi 2 -ntomp 10 -deffnm npt
14. Plotting Pressure of the system.
gmx energy -f npt.edr -o pressure.xvg
15. Plotting Density of the system.
gmx energy -f npt.edr -o density.xvg
16. Generating .tpr file; get md.mdp here
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
17. Running MD simulation.
gmx mdrun -v -pin on -ntmpi 2 -ntomp 10 -deffnm md_0_1
Please note -: It is just a tutorial for simplification of work flow detailed md tutorials can be found at http://www.mdtutorials.com/
This tutorial assumes you have GROMACS 2018 installed and working in a directory with input PDB file named as bound_protein.pdb. Using this you will make your protein ligand complex system followed by Temperature - Pressure Equilibration and Final production run on 10 cores.
GROMACS-2018
Before we star we would like you to remove the ligand molecule from your PDB file using any of your prefered softwares (VMD/PYMOL); Please save the protein molecule as a new file named as protein.pdb before starting.
1. Converting PDB input to GROMACS compatible file.
gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce
# This first step will make topology file on the basis of your selected forcefield and your protein of interest also it generates an atomic cordinate file for the protein.
2. Generating atomic for the ligand molecule
gmx editconf -f bound_protein.pdb -o bound_protein.gro
3. Generating cordinates and other parameters for the ligand molecule
#For this step we will be using PRODRG server which will geerate .itp file for your ligand.
4. Incorporating the atomic cordinates of the ligand molecule into the protein.gro file
The atomic cordinates can directly be incorporated in the "protein_processed.gro" file just below the last atom and remember to increase the number of atom counts in this file (found in the first line of the gro) by the number of atoms added in the form of ligand. Do the incorporation and save the file as complex.gro
The .itp file generated using the PRODRG server has to saved as ligand.itp file in your working directory
Finally to tell the topol.top file about the incorporation of ligand you need to do the following
1. Add the following lines just after posre.itp reference at the bottom of topol.top
------------------------------------------------
; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif
; Include ligand topology
#include "ligand.itp"
------------------------------------------------
2. Add the index of the ligand in the last line of the topol.top file (Replace the residue name of your ligand with XYZ)
Protein_chain_A 1
XYZ 1
2. Making a Box to make a boundary for box for simulation.
gmx editconf -f complex.gro -o protein_newbox.gro -c -d 1.0 -bt cubic
3. Adding water molecule to the system.
gmx solvate -cp protein_newbox.gro -cs spc216.gro -o protein_solv.gro -p topol.top
4. Generating .tpr file; get ions.mdp here
gmx grompp -f ions.mdp -c protein_solv.gro -p topol.top -o ions.tpr
5. Adding Ions to neutralised the system.
gmx genion -s ions.tpr -o protein_solv_ions.gro -p topol.top -pname NA -nname CL -neutral -conc 0.1
6. Generating .tpr file; get minim.mdp here
gmx grompp -f minim.mdp -c protein_solv_ions.gro -p topol.top -o em.tpr
7. Running Energy Minimization to re-arrange ions.
gmx mdrun -v -deffnm em
# sucess of this energy minimization step tells you that you did a good job
8. Plotting Potential of the system.
gmx energy -f em.edr -o potential.xvg
9. Generating .tpr file; get nvt.mdp here
gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr -r em.gro
10. Running Temperature Equilibrating.
gmx mdrun -v -pin on -ntmpi 2 -ntomp 10 -deffnm nvt
11. Plotting Temperature of the system.
gmx energy -f nvt.edr -o temperature.xvg
12. Generating .tpr file; get npt.mdp here
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -r nvt.gro
13. Running Pressure Equilibrating.
gmx mdrun -v -pin on -ntmpi 2 -ntomp 10 -deffnm npt
14. Plotting Pressure of the system.
gmx energy -f npt.edr -o pressure.xvg
15. Plotting Density of the system.
gmx energy -f npt.edr -o density.xvg
16. Generating .tpr file; get md.mdp here
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr -r npt.gro
17. Running MD simulation.
gmx mdrun -v -pin on -ntmpi 2 -ntomp 10 -deffnm md_0_1
Please note -: It is just a tutorial for simplification of work flow detailed md tutorials can be found at http://www.mdtutorials.com/