Run a tinker MD from XYZ input

run_tinker.sh

#!/usr/bin/env bash

source ~/modules/openbabel

cp $1 temp.xyz

babel -ixyz temp.xyz -osdf temp.sdf

sdf2tinkerxyz -k ../../mmff.key < temp.sdf

sed -i "s/verbose//" temp.xyz.key

~/opt/tinker/bin/dynamic.x temp.xyz.xyz -k temp.xyz.key 1000000 1.0 1.0 2 $2 | tee  trajectory.log | grep Instantaneous

rm -f all.xyz

shopt -s extglob

for f in temp.xyz.+([0-9]);
    do

        echo $f;

        ../../tinkerxyz2xyz.py $f > $f.xyz;

        calculate_rmsd --output $f.xyz temp.xyz > aligned_temp.xyz;

        cat aligned_temp.xyz >> all.xyz;

        # ../../xyz2om2 $f.xyz > $f\_om2.mop;
        # ../../xyz2orca $f.xyz > $f\_pbe0.inp;
        ../../xyz2om2_three_atoms $f.xyz > $f\_om2.mop;

        run_mndo99 $f\_om2.mop;

        rm -f aligned_temp.xyz $f\_om2.mop;

    done