Script for calculating covariance matrices

#!/bin/bash
##run cpptraj for cases where
##there are not covariance matrics

module load amber/14

for f in *.cpptraj;
do
    echo ${f}
    prefix=$(echo $f | cut -d. -f1);
    echo $prefix
    if [ -f ${prefix}_mwcovarmat.dat ]
    then
        echo "Found ${prefix}_mwcovarmat.dat";
        continue;
    fi
    cpptraj -i ${f};
done