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2_adgpu.sh
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#!/bin/bash
####===========================================================####
#### File Name: adgpu.sh ####
#### Author: szy && gj ####
#### E-mail: [email protected] ####
#### Date: 2020-10-15 16.03 ####
#### Last Modified: 2020-10-18 01.03 ####
#### Version: 2.0 ####
####===========================================================####
####prepare protein && protein autgrid
####change thing : basedir/ pdbname (vrk3)/ gridcenter /
tooldir="/opt/mgltools/1.5.7/MGLToolsPckgs/AutoDockTools/Utilities24"
range="50,50,50"
basedir="/home/jiexuan/slt/IRAK4/autodock-gpu_nrun100/"
ligdir="${basedir}/lig"
center="1.9,-15.32,-61.42"
# cd lig
# for lig in $(ls | grep mol2 );do
# ligname=$(basename ${lig} .mol2)
# # /opt/mgltools/1.5.7/bin/pythonsh $tooldir/prepare_ligand4.py -l ${lig} -o ${ligname}.pdbqt -A checkhydrogens
# done
# wait
# cd ..
cd lig
for lig in $(ls | grep pdbqt );do
ligname=$(basename ${lig} .pdbqt)
# /opt/mgltools/1.5.7/bin/pythonsh $tooldir/prepare_ligand4.py -l ${lig} -o ${ligname}.pdbqt -A checkhydrogens
done
wait
cd ..
for pdb in $(ls | grep pdb );do
pdbname=$(basename ${pdb} .pdb)
/opt/mgltools/1.5.7/bin/pythonsh $tooldir/prepare_receptor4.py -r $pdb -o $pdbname.pdbqt -A checkhydrogens -U nphs_lps_waters
done
# cd lig2
# for lig in $(ls | grep pdbqt );do
# # read -u 10
# {
# ligname=$(basename ${lig} .pdbqt)
# # python /opt/modules/mgltools/1.5.6@096b3c/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py -l ${lig} -o ${ligname}.pdbqt -A checkhydrogens
# # echo >&6
# }
# done
# cd ..
/opt/mgltools/1.5.7/bin/pythonsh ${tooldir}/prepare_gpf4.py -r $pdbname.pdbqt -o $pdbname.gpf -p npts="${range}" -p gridcenter="${center}" -p ligand_types="HD,HS,C,A,N,NA,OA,F,SA,S,P,Cl,Br,I"
/opt/autodock/gpu-1.5.3/bin/autogrid4 -p $pdbname.gpf
for ((j=0;j<8;j++));do ###ligand split step1
mkdir ${ligdir}/"temp"${j}
done
wait
echo "preparation is over"
cd ${ligdir}
a=1 ###ligand split step2
for file in $(ls | grep pdbqt );do
c=`expr $a % 8`
cp $file ${ligdir}/"temp"${c}/$file
a=`expr $a + 1`
done
b=`expr $a / 8`
echo "spliting is over (8 * ${b})"
echo "over"
cd ${basedir}
for ((j=0;j<8;j++));do
cd ${ligdir}/"temp"${j}
# {
for lig in $(ls | grep pdbqt );do
ligname=$(basename ${lig} .pdbqt)
/opt/autodock/gpu-1.5.3/bin/autodock_gpu_128wi -ffile ${basedir}/$pdbname.maps.fld -lfile ./${ligname}.pdbqt -devnum 1 -resnam ${ligname} -nrun 100
done
# }&
done
wait
# cd ${basedir}/result
# for dlg in $(ls | grep dlg );do
# y=$(basename ${dlg} .dlg)
# echo -n "${y}," >> ../score.txt
# a=$(awk -F ' ' '{print$4}' ${dlg} | tac | sed -n '4p')
# if [ $a ];then
# echo ${a} >> ../score.txt
# fi
# done
##for dlg in $(ls | grep dlg );do
##{
##dlgname=$(basename ${dlg} .dlg)
##pythonsh /opt/mgltools_x86_64Linux2_1.5.6/MGLToolsPckgs/AutoDockTools/Utilities24/write_conformations_from_dlg.py -d ${dlgname}.dlg
##}
##done
exit