# MD analysis for apo-protein is going wrong **URL:** \ **Category:** User discussions\ **Tags:** forcefield, grompp, mdrun, analysis-tools, simulation-setup\ **Created:** [May 20, 2024, 5:43am UTC](https://gromacs.bioexcel.eu/t/md-analysis-for-apo-protein-is-going-wrong/9175 "2024-05-20T05:43:23Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![era01](https://avatars.discourse-cdn.com/v4/letter/e/8e8cbc/32.png) [@era01](https://gromacs.bioexcel.eu/u/era01)\ **Post date:** [May 20, 2024, 5:43am UTC](https://gromacs.bioexcel.eu/t/md-analysis-for-apo-protein-is-going-wrong/9175/1 "2024-05-20T05:43:23Z")
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. ![Screenshot 2024-05-20 111649](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/3/3148a09c853f560bc367916a1b71f94604fe89f7.png) ---
**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\ **Post date:** [May 22, 2024, 8:51am UTC](https://gromacs.bioexcel.eu/t/md-analysis-for-apo-protein-is-going-wrong/9175/2 "2024-05-22T08:51:45Z")
Does it help if you do `gmx trjconv -s md_0_100.tpr -f md_0_100.xtc -n output.ndx -pbc nojump -o md_0_100_centered.xtc` instead of your current trjconv command? Or if you just use your `md_0_100.xtc` trajectory?