GROMACS-A Molecular Dynamic Approach

COMMANDS
1.perform the first command from lysozyme in water for cleaning your complex.

Note : 3HTB STANDS FOR PROTEIN AND JZ4 STANDS FOR LIGAND.

Command 2: grep JZ4 3HTB_clean.pdb > jz4.pdb

in your folder you will have a file named as JZ4.pdb which is the ligands .pdb format.
Now open your file 3HTB_clean.pdb in libre office and delete the part of ligand from that file and save it.

1. http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs (go on the link provided and download files)

2. first one is the charmm36-march2019.ff.tgz

3. second one is cgenff_charmm2gmx_ script file according to the version of python in your system. ( to check python version in a terminal type python –version)

4. also you need to download NetworkX application.(https://networkx.org/) use the provided link to download NetworkX version accoridng to your python version script that you have downloaded.

5. Keep the files downloaded in your folder.

Command 3: tar -zxvf charmm36-mar2019.ff.tgz(Unarchive the force field)

command 4: gmx pdb2gmx -f 3HTB_clean.pdb -o 3HTB_processed.gro

select option 1 (CHARMM36 all-atom force field (July 2017)

From ‘/usr/local/gromacs/share/gromacs/top’:) from all the list of forcefield.

6. https://cgenff.umaryland.edu/ go on the link provided and create an account on the server.

7.we have to produce .mol2 file to add hydrogen atom.

8.Several corrections must be made to jz4.mol2 before it can be used. Open jz4.mol2 in your favorite plain-text editor

9.The first change that needs to be made is in the MOLECULE heading. Replace “*****” with “JZ4,”

10. Next, fix the residue names and numbers such that they are all the same. This .mol2 file only contains one molecule, therefore there should only be one residue name and number specified. After editing, the corrected ATOM section of jz4.mol2 should read:

11.Command 5: perl sort_mol2_bonds.pl jz4.mol2 jz4_fix.mol2

12.command 6: python cgenff_charmm2gmx.py JZ4 jz4_fix.mol2 jz4.str charmm36-mar2019.ff

PLEASE NOTE: This script requires NetworkX package, version 1.11 – it is incompatible with NetworkX 2.x and will exit with a clear error.

13.Command 7: gmx editconf -f jz4_ini.pdb -o jz4.gro

14.command 8 :gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0

15.command 9:gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro

16. command 10:gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

(make a file in your folder with name ions.mdp and paste the below content )

17.Command 11: gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral

18.command 12 :(energy minimization): gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr

(make a file in your folder with name em.mdp and paste the below content )

19.Command 13: gmx mdrun -v -deffnm em

20.command 14 : gmx make_ndx -f jz4.gro -o index_jz4.ndx ( after this command you wont get a command line as the command is not yet complete.)

To complete the command type
> 0 & ! a H* (now enter)
> q (type this and enter then the command line will appear.)

21.command 15: gmx genrestr -f jz4.gro -n index_jz4.ndx -o posre_jz4.itp -fc 1000 1000 1000
22.Command 16: gmx make_ndx -f em.gro -o index.ndx
23.command 17 : gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n index.ndx -o nvt.tpr
(make a file in your folder with name nvt.mdp and paste the below content )

24.Command 18: gmx mdrun -deffnm nvt

25.command 19 :gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx -o npt.tpr

(make a file in your folder with name npt.mdp and paste the below content )

26.Command 20: gmx mdrun -deffnm npt

27.command 21: gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index.ndx -o md_0_10.tpr

(make a file in your folder with name md.mdp and paste the below content )

28.Command 22: gmx mdrun -deffnm md_0_10

( the simulation can take upto days to complete the process as its running for 10ns)
have patience and don’t shut down the pc)

If you want to change the nano second from 10 to any number just multiply that nano second with 500000 and ps with 1000 and change the number with the green highlighted number in the md.mdp file above.