GROMACS version:2023.1
GROMACS modification: Yes/No
Here post your question
hello. I am getting some problems regarding the simulation of my apoprotein. I did md simulation for 7 different protein and 1 common ligand. and then I performed apo protein md simulation for those 7 proteins. I followed the ‘lysosome in water’ tutorial. for some reason, I am encountering problems. like in a few of the proteins while plotting the rmsf vales the residue numbers don’t match for the apoprotein and complex [of same protein]. and in few proteins I am getting apo-proteins rmsd value less than that of rmsd value of complex. this shouldn’t have occurred.
here are the commands I have used for apo protein md run :
gmx pdb2gmx -f final.pdb -o processed.gro -ter -ignh
gmx editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt cubic
gmx solvate -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -neutral
gmx grompp -f minim.mdp -c solv_ions.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em
gmx make_ndx -f em.gro -o index.ndx
1
gmx make_ndx -f processed.gro -n index.ndx -o output.ndx
1 & a 1-1219
1 & a 1220-2509
gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -n output.ndx -o nvt.tpr
gmx mdrun -v -deffnm nvt
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n output.ndx -o npt.tpr -maxwarn 2
gmx mdrun -v -deffnm npt
gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n output.ndx -o md_0_100.tpr
gmx mdrun -v -deffnm md_0_100
gmx trjconv -s md_0_100.tpr -f md_0_100.xtc -n output.ndx -center -ur compact -pbc mol -o md_0_100_centered.xtc
(18 & 0)
gmx rms -s md_0_100.tpr -f md_0_1001_centered.xtc -o rmsd1.xvg -tu ns
(4 & 4)
gmx rmsf -s md_0_100.tpr -f md_0_100_centered.xtc -n index.ndx -o apormsf.xvg -res
(3)
gmx hbond -s md_0_100.tpr -f md_0_100_centered.xtc -n index.ndx -num hb.xvg -tu ns
(1 & 1)
gmx sasa -f md_0_100_centered.xtc -s md_0_100.tpr -n index.ndx -o sasa.xvg -tu ns
(1)
gmx gyrate -s md_0_100.tpr -f md_0_100_centered.xtc -o gyrate.xvg
1
the graph is the rmsf of 5n92 protein. in x axis there is residue number. the red one is the complex and black one is the apo protein
someone please help regarding this issue. would be really grateful if anyone could help.
