Mywork=/home/zjxu/ylshi/SARS-CoV-2-process
index=$1
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/zjxu/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/zjxu/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/home/zjxu/anaconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/zjxu/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

for Protein in `cat $index`
do
conda activate pdb2pqr
pdb2pqr_cli --ff=amber --ffout=amber --chain --with-ph=7 ${Mywork}/Protein/${Protein}.pdb ${Mywork}/Protein/${Protein}_H.pqr
#obabel -ipqr  ${Mywork}/Protein/${Protein}_H.pqr -o pdb -O ${Mywork}/Protein/${Protein}_H.pdb
conda activate mgltools
prepare_receptor4.py -r ${Mywork}/Protein/${Protein}_H.pqr -o ${Mywork}/Protein/${Protein}.pdbqt -C -U nphs_lps_waters_nonstdres
done