#!/bin/bash

set -e

BASE="/home/databank/ydn/DRAK2/MD-DRAK2/DCA-16C/Mg/system/"

for md in md1 md2 md3 md4
do

echo "====================================="
echo "Processing ${md}"
echo "====================================="


cd ${BASE}/${md}/analysis/RMSD || exit 1

mkdir -p rmsd_analysis_refit


cpptraj << CPPTRAJ

parm ../../../parameters/native.prmtop

reference ../../../parameters/com-dry.pdb

trajin dry-align.xtc


# fit protein CA to same reference
rms Fit reference :1-291@CA


# protein RMSD
rms Protein reference :1-291@CA nofit \
out rmsd_analysis_refit/protein.dat


# ligand RMSD
rms Ligand reference :293&!@H= nofit \
out rmsd_analysis_refit/ligand.dat


# complex RMSD (protein+Mg+ligand)
rms Complex reference :1-293&!@H= nofit \
out rmsd_analysis_refit/complex.dat


run

quit

CPPTRAJ



echo "Generating combined file..."

paste \
<(awk '!/^#/{print n++}' rmsd_analysis_refit/protein.dat) \
<(awk '!/^#/{print $2}' rmsd_analysis_refit/protein.dat) \
<(awk '!/^#/{print $2}' rmsd_analysis_refit/ligand.dat) \
<(awk '!/^#/{print $2}' rmsd_analysis_refit/complex.dat) \
> rmsd_analysis_refit/rmsd-combined.dat


echo "${md} finished."

done


echo "====================================="
echo "ALL DONE"
echo "====================================="