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gmxpbsa1.sh
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gmxpbsa1.sh
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#!/bin/bash
# GMXPBSA tool is free software. You can redistribute it and/or modify it under the GNU Lessere General Public Lincese as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version (http://www.gnu.org/licenses/lgpl-2.1.html).
# GMXPBSA is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
# For any problem, doubt, comment or suggestion please contact me at [email protected] or [email protected]
# Copyright 2013 Dimitrios Spiliotopoulos, Cristina Paissoni
#export LC_NUMERIC="en_US.UTF-8"
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
source $DIR/function_base.dat
#@@@@@@@@@@@@@@@@@@@#
# (0) Print version #
#@@@@@@@@@@@@@@@@@@@#
if ! [ $# -eq 0 ];then
if [ $1 == "-h" ]; then
clear
echo -e "\n\nGMXPBSA version 2.1.2_dev\n\n"
exit
fi
fi
clear
check INPUT.dat ERROR_NO_INPUT
set_variable_default_run "run" "1";
set_variable "root";
RUN=RUN${run}_$root
if [ -d $RUN ]; then
cp -r $RUN backup0_$RUN;
cd $RUN
# create the new files "REPORTFILE1 / WARNINGS_gmxpbsa1"
if [ -f REPORTFILE1 ] ; then
rm REPORTFILE1
fi
if [ -f WARNINGS_gmxpbsa1.dat ] ; then
rm WARNINGS_gmxpbsa1.dat
fi
cd ..
set_variable_default1 "cluster" "n" "$RUN/REPORTFILE1";
set_variable_default1 "mnp" "1" "$RUN/REPORTFILE1";
# set_variable_default1 "nodes" "1" "$RUN/REPORTFILE1";
# set_variable_default1 "mem" "5GB" "$RUN/REPORTFILE1";
set_variable_default1 "multitrj" "n" "$RUN/REPORTFILE1";
if [ $multitrj == "y" ]; then
set_variable_multiple "root_multitrj";
N_start_dir=`echo $root_multitrj | awk '{N=split($0,v," "); print N}'`
for ((i=0; i<$N_start_dir; i++)); do
start_dir[$i]=`echo $root_multitrj | awk -v i=$(($i+1)) '{N=split($0,v," "); print v[i]}'`
done
fi
cd $RUN
cp ../INPUT.dat ./run${run}_parameters_1.in
if [ -f run${run}_parameters.in ]; then
check_INPUT=`diff -e run${run}_parameters.in run${run}_parameters_1.in | head -n 1 | cut -d " " -f1`;
else
mv run${run}_parameters_1.in run${run}_parameters.in
fi
if [ -z $check_INPUT ]; then rm -f run${run}_parameters_1.in; else echo -e "\nWARNING!! The INPUT file you are using now is different from the one you used running \"gmxpbsa0.sh\"\n"; fi
else
echo -e "\n"$(date +%H:%M:%S)"\n The directory $RUN is not present. Please check the INPUT.dat file or run \"gmxpbsa0.sh\"."
echo "Exiting --"
exit
fi
rm -f \#* *~
if [ $multitrj == "y" ]; then
FolderFile=$(for ((i=0;i<$N_start_dir; i++)); do ls -1| grep "^${start_dir[$i]}"; done | sed s/" "/"\n"/g | sort -u)
else
FolderFile=$(ls -1 | grep "^$root")
fi
for Folder in $FolderFile; do
# Check that gmxpbsa0.sh ended correctly.
if [ ! -e DONE0_$Folder ]; then
echo -e "\n"$(date +%H:%M:%S)" \n ERROR: I could not find DONE0_$Folder, probably something went wrong with gmxpbsa0.sh. Please check or re-run it. \n" | tee -a REPORTFILE1
echo "Exiting -- please read the REPORTFILE1"
exit
fi
# Check that in all the directories "MD_*" there is the sub-directory "APBS_CALCULATIONS"
cd $Folder
check APBS_CALCULATIONS ../REPORTFILE1
cd ..
done
for Folder in $FolderFile; do
rm -f DONE0_$Folder;
done
# Cycle on all the directories called "$root*/APBS_CALCULATIONS"
for Folder in $FolderFile; do
cd $Folder
cd APBS_CALCULATIONS
# In this directory we have to do ($calc) apbs calculations. Then, considering that we can use maximum $mnp processors, we will have to repeat the "qsubbing" $D times.
calc=$(ls comp*.pqr | wc | awk '{print $1}')
let "D=$calc/$mnp"
let "R=$calc%$mnp"
if [ $R -eq 0 ]; then let "D=$D-1" ; fi
if [ $calc -lt $mnp ]
then
let "D=0"
let "mnp=$calc"
fi
# if NO cluster
if [ $cluster == "n" ]
then
echo -e "\n\n$(date +%H:%M:%S) Starting the APBS CALCULATIONS in $Folder directory\n" | tee -a ../../REPORTFILE1
command=bash
#for each group of calculations that must be submitted in the same time create a file
for (( f=0;f<=$D; f++ )); do
echo -e "#!/bin/bash\n" > file_APBS_$f.sh
for ((k=0;k<$mnp;k++)); do
let "index[$k]=($mnp*$f)+$k"
C=0
if [ -f apbs${index[$k]}.sh ]; then echo -ne "bash apbs${index[$k]}.sh" >> file_APBS_$f.sh; fi
let "ind=${index[$k]}+1"
if [ -f apbs$ind.sh ]; then C=1; fi
let "kmax=$mnp-1"
if [ $k -lt $kmax ] && [ $C -eq "1" ] ; then
echo -ne " & ">> file_APBS_$f.sh;
else
echo -e "\nwait" >> file_APBS_$f.sh;
fi
done
if [ $f -eq 0 ]; then res1=$(date +%s); fi
chmod u+x file_APBS_$f.sh
bash file_APBS_$f.sh
if [ $f -eq 0 ]; then
res2=$(date +%s)
dt_each=$(echo "$res2 - $res1" | bc )
F=$(($D+1))
dt=$(echo "(${dt_each}+3)*$F" | bc )
day=$(echo "$dt/86400" | bc )
dt2=$(echo "$dt-86400*$day" | bc)
h=$(echo "$dt2/3600" | bc )
dt3=$(echo "$dt2-3600*$h" | bc )
dm=$(echo "$dt3/60" | bc )
printf "The total time estimated for the APBS calculations in the folder $Folder is %02d days %02d hours and %02d minutes\n\n" $day $h $dm | tee -a ../../REPORTFILE1
fi
rm -f file_APBS_$f.sh
let "group=$f+1"
echo -e "$(date +%H:%M:%S) In $Folder directory the $group-th group of $mnp apbs calculations was completed" | tee -a ../../REPORTFILE1
done
echo -e "$(date +%H:%M:%S) In $Folder directory all apbs*.sh completed for polar solvation calculations" | tee -a ../../REPORTFILE1
for file in Hapbs*.sh; do
Hcal=`bash $file`
done
echo -e "$(date +%H:%M:%S) In $Folder directory Hapbs*.sh completed for nonpolar solvation calculations" | tee -a ../../REPORTFILE1
else
command=qsub
fi
# if YES cluster
if [ $cluster == "y" ]
then
# cycle on $mnp
#let "Mnp=$mnp-1"
echo -e "\n\n$(date +%H:%M:%S) Starting the APBS CALCULATIONS in $Folder directory\n" | tee -a ../../REPORTFILE1
MAX_JOBS=5; #It will be 3*2=6 jobs, 3 for polar/ 3 for non-polar calculations
let "NGroups=($D+1)/$MAX_JOBS"
let "RR=($D+1)%$MAX_JOBS"
if [ $RR -eq 0 ]; then let "NGropus=$NGroups-1" ; fi
iter=0
for group in `seq 0 $NGroups`; do
let "first_apbs=$group*$MAX_JOBS"
let "last_apbs=(($group+1)*$MAX_JOBS)-1"
if [ $group -eq $NGroups ]; then last_apbs=$D ; fi
for j in `seq $first_apbs $last_apbs`; do
if [ $j -eq $first_apbs ]; then
eval "Pcalc[$j]=`$command apbs$j.sh`"
echo -e "$(date +%H:%M:%S) In $Folder directory apbs$j.sh submitted for polar solvation calculations" | tee -a ../../REPORTFILE1
eval "Hcalc[$j]=`$command -W depend=afterok:${Pcalc[$j]} Hapbs$j.sh`"
echo -e "$(date +%H:%M:%S) In $Folder directory Hapbs$j.sh submitted for nonpolar solvation calculations" | tee -a ../../REPORTFILE1
else
let "k=$j-1"
eval "Pcalc[$j]=`$command -W depend=afterok:${Hcalc[$k]} apbs$j.sh`"
echo -e "$(date +%H:%M:%S) In $Folder directory apbs$j.sh submitted for polar solvation calculations" | tee -a ../../REPORTFILE1
eval "Hcalc[$j]=`$command -W depend=afterok:${Pcalc[$j]} Hapbs$j.sh`"
echo -e "$(date +%H:%M:%S) In $Folder directory Hapbs$j.sh submitted for nonpolar solvation calculations" | tee -a ../../REPORTFILE1
fi
done
pid_1=`echo ${Hcalc[$last_apbs]}| cut -d . -f1`
res1=$(date +%s)
while [ $iter -le $group ]
do
check=`qstat $pid_1 2> /dev/null | wc -l`
sleep 5s
if [ $check == 0 ]; then
iter=$[$iter+1]
if [ $iter -eq 1 ]; then
res2=$(date +%s)
dt_each=$(echo "$res2 - $res1" | bc )
F=$(($NGroups+1))
dt=$(echo "${dt_each}*$F" | bc )
day=$(echo "$dt/86400" | bc )
dt2=$(echo "$dt-86400*$day" | bc)
h=$(echo "$dt2/3600" | bc )
dt3=$(echo "$dt2-3600*$h" | bc )
dm=$(echo "$dt3/60" | bc )
printf "\nThe total time estimated for the APBS calculations in the folder $Folder is %02d days %02d hours and %02d minutes\n" $day $h $dm | tee -a ../../REPORTFILE1
fi
fi
done
done
fi
# check that everything goes in the right way
rm -f Completed_frame.dat Failed_frame.dat
echo -e "\n\n" | tee -a ../../REPORTFILE1
for ((j=0; j<$calc;j++)); do
if [ -f Hstru$j.out ]; then
checkH=$( echo $( awk '/Global net APOL energy/ {print $6}' Hstru$j.out) | bc -l )
if [ ${checkH} ]; then
echo -e "In $Folder directory Hapbs calculations completed for the $j-th structure" | tee -a ../../REPORTFILE1
echo -e "Hapbs frame $j" >> Completed_frame.dat
else
echo -e "WARNING!!! In $Folder directory Hapbs calulation relative to frame $j is not completed. Please take a look to this frame and try to do this calculation manually." | tee -a ../../REPORTFILE1 ../../WARNINGS_gmxpbsa1.dat
echo -e "Hapbs frame $j" >> Failed_frame.dat
fi
else
echo -e "WARNING!!! In $Folder directory Hapbs calulation relative to frame $j did not start. Please take a look to this frame and try to do this calculation manually." | tee -a ../../REPORTFILE1 ../../WARNINGS_gmxpbsa1.dat
echo -e "Hapbs frame $j" >> Failed_frame.dat
fi
if [ -f stru$j.out ]; then
checkP=$( echo $( awk '/Global net ELEC energy/ {print $6}' stru$j.out) | bc -l )
if [ ${checkP} ]; then
echo -e "In $Folder directory apbs calculations completed for the $j-th structure" | tee -a ../../REPORTFILE1
echo -e "apbs frame $j" >> Completed_frame.dat
else
echo -e "WARNING!!! In $Folder directory apbs calulation relative to frame $j is not completed. Please take a look to this frame and try to do this calculation manually." | tee -a ../../REPORTFILE1 ../../WARNINGS_gmxpbsa1.dat
echo -e "apbs frame $j" >> Failed_frame.dat
fi
else
echo -e "WARNING!!! In $Folder directory apbs calulation relative to frame $j did not start. Please take a look to this frame and try to do this calculation manually." | tee -a ../../REPORTFILE1 ../../WARNINGS_gmxpbsa1.dat
echo -e "apbs frame $j" >> Failed_frame.dat
fi
done
if [ ! -f Failed_frame.dat ];
then
touch ../../DONE1_$Folder;
else
failed_apbs=`grep "^apbs" Failed_frame.dat | wc -l`
failed_Hapbs=`grep "^Hapbs" Failed_frame.dat | wc -l`
perc_apbs=$(echo "scale=2; $failed_apbs*100/$calc" | bc -l)
perc_Hapbs=$(echo "scale=2; $failed_Hapbs*100/$calc" | bc -l)
echo -e "$(date +%H:%M:%S): WARNING!!! In $Folder directory there are $failed_apbs APBS failed frames ($perc_apbs% of the total frames) and $failed_Hapbs HAPBS failed frames ($perc_Hapbs% of the total frames). Please check them!\nIf you want to try to recover them in gmxpbsa2.sh set the option \"RecoverJobs\" to \"y\" in the INPUT.dat file.\n" | tee -a ../../REPORTFILE1
fi
cd ../..
done
cd ..