RSV——calculate_rmsd计算Rmsd

#!/bin/bash

#refer_pdb=$1
#cd Motif_backbone

mkdir ChainA
for i in *.pdb;
do
    python ParsePDB_outputA.py $i > ChainA/$i
done


cd ChainA
pdblist=( d0040.pdb  d0071.pdb  d0251.pdb  d0276.pdb  d0399.pdb  d0429.pdb  
          d0518.pdb  d0542.pdb  d0627.pdb  d0665.pdb  d0683.pdb  d0810.pdb  
          d0850.pdb  d0935.pdb  d0967.pdb  d0064.pdb  d0142.pdb  d0267.pdb  
          d0283.pdb  d0400.pdb  d0483.pdb  d0525.pdb  d0608.pdb  d0658.pdb  
          d0676.pdb  d0803.pdb  d0836.pdb  d0904.pdb  d0952.pdb  d0988.pdb )
for i in ${pdblist[@]};
do
    name=${i%%.*}
    calculate_rmsd --reorder ${name}_last.pdb ${name}_start.pdb | awk -v name="$name" '{printf "%s %8f\n", name, $0}' >> MD_chainA_rmsd
done

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2. python rmsd包， calculate_rmsd命令的 --reorder选项不可轻易使用