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GMX Com

This document outlines the steps to prepare a protein-ligand system for molecular dynamics simulation using GROMACS. It describes preparing the topology, solvating and adding ions to the system, equilibrating using EM, NVT, NPT, and production MD simulations, and analyzing the results through RMSD, RMSF, and energy calculations.

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Himanshu Bisht
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58 views

GMX Com

This document outlines the steps to prepare a protein-ligand system for molecular dynamics simulation using GROMACS. It describes preparing the topology, solvating and adding ions to the system, equilibrating using EM, NVT, NPT, and production MD simulations, and analyzing the results through RMSD, RMSF, and energy calculations.

Uploaded by

Himanshu Bisht
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as TXT, PDF, TXT or read online on Scribd
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;gmx pdb2gmx -f clean_model.pdb -o model.

gro -water spc


;gmx editconf -f model.gro -o box.gro -d 0.8 -bt cubic
;gmx solvate -cp box.gro -cs spc216.gro -o solv.gro -p topol.top
;gmx grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr -maxwarn 3
;gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral
-conc 0.2
;gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr
;gmx mdrun -v -deffnm em
;gmx grompp -f em-cg.mdp -c em.gro -p topol.top -o em-cg.tpr
;gmx mdrun -v -deffnm em-cg -nt 4
;gmx grompp -f nvt.mdp -c em-cg -r em-cg.gro -p topol.top -o nvt.tpr -maxwarn 3
;gmx mdrun -deffnm nvt
;gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr -
maxwarn 3
;gmx mdrun -deffnm npt
;gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0.tpr
;gmx mdrun -deffnm md_0
;gmx trjconv -s md_0.tpr -f md_0.xtc -o md_0PBC.xtc -pbc mol -center (1and0)

;gmx rms -s md_0.tpr -f md_0PBC.xtc -o rmsd.xvg -tu ns (4 and 4)


;xmgrace rmsd.xvg
;gmx rmsf -f md_0.xtc -s md_0.tpr -o rmsf.xvg -oq bfac.pdb
;xmgrace rmsf.xvg
;pymol bfac.pdb

;Initital Structure: gmx rms -s em.tpr -f md_0PBC.xtc -o rmsd_xtal.xvg -tu ns


(Choose 4 and 4)
;Structure post MD: gmx rms -s md_0.tpr -f md_0PBC.xtc -o rmsd.xvg -tu ns (Choose 4
and 4)

;Plot the two together using Xmgrace: xmgrace rmsd_xtal.xvg rmsd.xvg

;( where em.tpr is the initial structure and md_0.tpr is after nvt npt and md)
;Black = New Structure; Red =Old Structure

;gmx trjconv -f em.gro -o em.pdb -pbc mol -s em.tpr (gmx to pdb ) (select 1)
; gmx pdb2gmx -f em.pdb -water spce -ignh ( if error occurs)

;gmx energy -s em-cg.tpr -f md_0.edr -o pos.xvg


;xmgrace pos.xvg

obabel inverted_Q1lig1.pdb -O lig2.pdbqt

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