RMSD

cd /home/databank/ydn/DRAK2/analysis/check/RMSD-fir


CPPTRAJ="/home/dddc/software/miniforge3/envs/ambertools/bin/cpptraj"
TOPO="/home/databank/ydn/DRAK2/MD/Re/noMg/system1/parameters/native.prmtop"
TRAJ="/home/databank/ydn/DRAK2/MD/noMg/system1/md_500ns/analysis/RMSD/dry-align.xtc"


$CPPTRAJ << 'EOF'
parm /home/databank/ydn/DRAK2/MD/Re/noMg/system1/parameters/native.prmtop
trajin /home/databank/ydn/DRAK2/MD/noMg/system1/md_500ns/analysis/RMSD/dry-align.xtc 1 1
trajout ref_md6.pdb pdb
run
quit
EOF


$CPPTRAJ << 'EOF'
parm /home/databank/ydn/DRAK2/MD/Re/noMg/system1/parameters/native.prmtop
trajin /home/databank/ydn/DRAK2/MD/noMg/system1/md_500ns/analysis/RMSD/dry-align.xtc
reference ref_md6.pdb [ref]
rms protein_rmsd ref [ref] :1-291@CA,C,N out rmsd-protein-md6.dat
rms fit_protein ref [ref] :1-291@CA,C,N
rms ligand_rmsd ref [ref] :292 nofit out rmsd-mol-md6.dat
rms complex_rmsd ref [ref] :1-292 nofit out rmsd-complex-md6.dat
run
quit
EOF


paste rmsd-protein-md6.dat rmsd-mol-md6.dat rmsd-complex-md6.dat \
    | awk 'NR>1 {print $1, $2, $4, $6}' > rmsd-combined-md6.dat
echo "md6完成"