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ProteinMC
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#!/bin/bash
#########################################################################
# proteinMC, Version 1.0.0
# 2022, ShanghaiTech University, Wang Lin
# Email: [email protected]
#########################################################################
CPU_HOST=CPU
NJOBS=30
Job_Type="MC"
Force_Field="S-OPLS"
Rosetta_score="ref2015_cart"
backbone_sampling="yes"
SCHRODINGER=${SCHRODINGER}
MC_Steps=50
output_num=3
random_seed=yes
use_membrane="no"
Range="all"
constraints=false
constraints_force=10.00
constraints_tolerance=0.00
rosetta_app=${rosetta_app}
rosetta_db=${rosetta_db}
rosetta_version=mpi # the install version of rosetta: mpi or static.
MPI_mode=false
comp1="A"
comp2="B"
help(){
cat << EOF
Prime Monte Carlo simulation.
Usage: proteinMC -i <structure>.mae -s 100 -r -H <CPU> -N 30
Required Options:
-i Input sturctural file in *.mae or dir for *.pdb, required.
-t Job type for Monte Carlo simulation: <${Job_Type}>
Protein Prepare:
Normal, protein prepare for normal tissue and sub-celluar location.
Lysozyme, protein prepare for lysozyme.
Prime Global Refinement:
MC, hybird MC;
SIDE_PRED, sidechain refine with backbone sampling.
SIDE_OPT, sidechain refine without backbone sampling.
Rosetta Global Refinement:
Fast_Relax, protein all-atom relax with backbone sampling.
Relax, large cycle number fast relax.
PPI_Relax, relax protein-protein interface.
PPI refinement:
PPI_MMGBSA, MM-GBSA for protein-protein interface.
FlexPepDock, protein-peptide global docking.
FlexPepRefine, protein-peptide local refinement.
PPI_Dock, protein-protein global docking.
PPI_Refine, protein-protein docking refinement.
Environment Options (MC, SIDE_PRED, SIDE_OPT, and PPI_MMGBSA):
-m Use this option to consider the membrane in the simulation,
which requires setting the membrane position in GUI.
PPI Refinement Options (PPI_MMGBSA, FlexPepDock, FlexPepRefine, PPI_Dock and PPI_Refine):
-1 The asl (for prime) or chain name (for rosetta) of component 1 (receptor). <${comp1}>
-2 The asl (for prime) or chain name (for rosetta) of component 2 (ligand or peptide). <${comp2}>
Prime Global Refinement Options (MC, SIDE_PRED, and SIDE_OPT):
-R ASL for refine range. <${Range}>
-s Steps of MC simulations. <${MC_Steps}>
-r Use the random seed. <${random_seed}>
-c Set the position constraints for a ASL, such as "backbone".
-f Set the force for position constraints. <${constraints_force}>
-d Set the distance tolerance for position constraints. <${constraints_tolerance}>
Output Options:
-n Number of output conformation per input structure. <${output_num}>
Job Control Options:
-H Host for CPU queue. <${CPU_HOST}>
-S Path to your Schrodinger package. <${SCHRODINGER}>
-A Path to rosetta app, default version is mpi. <${rosetta_app}>
-B Path to rosetta database. <${rosetta_db}>
-N Number of subjobs(CPU cores). <${NJOBS}>
Thank you for your using, If you found any problem, Please contact [email protected].
EOF
}
while getopts ":hi:s:H:S:N:ms:rn:c:f:d:R:t:A:B:1:2:" opt
do
case $opt in
h)
help
exit;;
H)
CPU_HOST=$OPTARG;;
N)
NJOBS=$OPTARG;;
S)
SCHRODINGER=$OPTARG;;
i)
input_file=`readlink -f $OPTARG`;;
t)
Job_Type=$OPTARG;;
m)
use_membrane="yes";;
s)
MC_Steps=$OPTARG;;
r)
random_seed="yes";;
n)
output_num=$OPTARG;;
1)
comp1=$OPTARG;;
2)
comp2=$OPTARG;;
c)
constraints=true
constraints_asls=$OPTARG;;
f)
constraints_force=$OPTARG;;
d)
constraints_tolerance=$OPTARG;;
R)
Range=$OPTARG;;
A)
rosetta_app=$OPTARG;;
B)
rosetta_db=$OPTARG;;
?)
echo ""
echo "Error: Do not use undefined options."
echo ""
help
exit;;
esac
done
function PrimeMC(){
job_name="$(basename ${input_file%%.*})_${Job_Type}"
if [ ${CPU_HOST} == "localhost" ] || [ ${CPU_HOST} == "local" ];then
waitcmd="-WAIT"
else
waitcmd=""
fi
if [ ${input_file##*.} == "mae" ] || [ ${input_file##*.} == "maegz" ];then
echo ""
elif [ ${input_file##*.} == "pdb" ];then
$SCHRODINGER/utilities/structconvert ${input_file} $(basename ${input_file%%.*}).mae
export input_file=`readlink -f $(basename ${input_file%%.*}).mae`
elif [ -d ${input_file} ];then
$SCHRODINGER/utilities/structcat -ipdb ${input_file}/*.pdb -omae ${job_name}_in.mae
export input_file=`readlink -f ${job_name}_in.mae`
fi
if [ ${Job_Type} == "Normal" ];then
echo "Protein Prepare....."
${SCHRODINGER}/utilities/prepwizard -fillsidechains -disulfides -rehtreat -epik_pH 6.9 -epik_pHt 0.6 -samplewater -propka_pH 6.9 -f S-OPLS -rmsd 0.3 -WAIT -keepfarwat -glycosylation -delwater_hbond_cutoff 3 ${input_file} ${job_name}-prep.maegz
elif [ ${Job_Type} == "Lysozyme" ];then
echo "Protein Prepare....."
${SCHRODINGER}/utilities/prepwizard -fillsidechains -disulfides -rehtreat -epik_pH 4.75 -epik_pHt 0.75 -samplewater -propka_pH 4.75 -f S-OPLS -rmsd 0.3 -WAIT -keepfarwat -glycosylation -delwater_hbond_cutoff 3 ${input_file} ${job_name}-prep.maegz
elif [ ${Job_Type} == "PPI_MMGBSA" ];then
echo "
Set up a MM-GBSA calculation:
Use_membrane: ${use_membrane}
"
if [ ${use_membrane} == "yes" ];then
${SCHRODINGER}/prime_mmgbsa -job_type REAL_MIN -rflexdist 5 -jobname "${job_name}-MMGBSA" -ligand "${comp2}" -membrane -HOST "${CPU_HOST}:${NJOBS}" -NJOBS ${NJOBS} ${waitcmd} ${input_file}
else
${SCHRODINGER}/prime_mmgbsa -job_type REAL_MIN -rflexdist 5 -jobname "${job_name}-MMGBSA" -ligand "${comp2}" -HOST "${CPU_HOST}:${NJOBS}" -NJOBS ${NJOBS} ${waitcmd} ${input_file}
fi
else
echo "
Set up a Prime ${Job_Type} simulation:
Refine_Range: ${Range}
Use_random_seed: ${random_seed}
Use_membrane: ${use_membrane}
Use_constraints: ${constraints}
Steps: ${MC_Steps}
"
if [ ${Job_Type} == "MC" ];then
cat << EOF > ${job_name}.inp
STRUCT_FILE ${input_file}
JOB_TYPE REFINE
PRIME_TYPE MC
SELECT asl=${Range}
NSTEPS ${MC_Steps}
PROB_SIDEMC 0.000000
PROB_RIGIDMC 0.000000
PROB_HMC 1.000000
TEMP_HMC 900.000000
FIND_BEST_STRUCTURE yes
NUM_OUTPUT_STRUCT ${output_num}
USE_CRYSTAL_SYMMETRY no
USE_RANDOM_SEED ${random_seed}
SEED 0
OPLS_VERSION ${Force_Field}
EXT_DIEL 80.00
USE_MEMBRANE ${use_membrane}
EOF
elif [ ${Job_Type} == "SIDE_PRED" ];then
cat << EOF > ${job_name}.inp
STRUCT_FILE ${input_file}
JOB_TYPE REFINE
PRIME_TYPE SIDE_PRED
SELECT asl=${Range}
NUM_SC_OUTPUT_STRUCT ${output_num}
USE_CRYSTAL_SYMMETRY no
USE_RANDOM_SEED ${random_seed}
SEED 0
OPLS_VERSION ${Force_Field}
EXT_DIEL 80.00
USE_MEMBRANE ${use_membrane}
SAMPLE_BACKBONE ${backbone_sampling}
BACKBONE_LEN 3
EOF
fi
if [ ${constraints} == true ];then
echo "CONSTRAINT_0 asl=${constraints_asls};${constraints_force};${constraints_tolerance}" >> ${job_name}.inp
fi
${SCHRODINGER}/prime -HOST "${CPU_HOST}:${NJOBS}" -NJOBS ${NJOBS} ${waitcmd} ${job_name}.inp
fi
}
function RosettaMC(){
job_name="$(basename ${input_file%%.*})_${Job_Type}"
mkdir -p ${job_name}_OUT
echo "
Set up a Rosetta MC simulation:
nstruct for per input: ${output_num}
output directory: ${job_name}_OUT
"
if [ ${input_file##*.} == "mae" ] || [ ${input_file##*.} == "maegz" ];then
mkdir -p $(basename ${input_file%%.*})
$SCHRODINGER/utilities/structconvert -split-nstructures 1 ${input_file} $(basename ${input_file%%.*})/$(basename ${input_file%%.*}).mae
ls $(basename ${input_file%%.*})/$(basename ${input_file%%.*})-*.mae | parallel -j 1 $SCHRODINGER/utilities/structconvert $(basename ${input_file%%.*})/{} $(basename ${input_file%%.*})/{.}.pdb
ls $(basename ${input_file%%.*})/*.pdb | parallel -j 1 echo "$(basename ${input_file%%.*})/{}" >> ${job_name}_input.list
elif [ ${input_file##*.} == "pdb" ];then
export MPI_mode=true
elif [ -d ${input_file} ];then
ls ${input_file} | parallel -j 1 echo "${input_file}/{}" >> ${job_name}_input.list
fi
if [ ${CPU_HOST} == "CPU" ];then
cat << EOF > ${job_name}.pbs
#PBS -N ${job_name}
#PBS -l nodes=1:ppn=${NJOBS}:centos7
#PBS -S /bin/bash
#PBS -j oe
#PBS -l walltime=360:00:00
#PBS -q siais_pub_cpu
module load mpi/openmpi/4.1.1
module load compiler/gnu/8.3.0
cd \$PBS_O_WORKDIR
EOF
elif [ ${CPU_HOST} == "amdnode" ];then
cat << EOF > ${job_name}.pbs
#PBS -N ${job_name}
#PBS -l nodes=1:ppn=${NJOBS}
#PBS -S /bin/bash
#PBS -j oe
#PBS -l walltime=360:00:00
#PBS -q amdnode
module load mpi/openmpi/4.1.1
module load compiler/gnu/8.3.0
cd \$PBS_O_WORKDIR
EOF
elif [ ${CPU_HOST} == "fat" ];then
cat << EOF > ${job_name}.pbs
#PBS -N ${job_name}
#PBS -l nodes=1:ppn=${NJOBS}
#PBS -S /bin/bash
#PBS -j oe
#PBS -l walltime=360:00:00
#PBS -q pub_fat
module load mpi/openmpi/4.1.1
module load compiler/gnu/8.3.0
cd \$PBS_O_WORKDIR
EOF
else
echo "Error: Rosetta job cannot run on ${CPU_HOST}"
fi
if [ ${Job_Type} == "FlexPepDock" ] || [ ${Job_Type} == "FlexPepRefine" ] || [ ${Job_Type} == "PPI_Dock" ] || [ ${Job_Type} == "PPI_Refine" ]; then
if [ ${MPI_mode} == "true" ];then
if [ ${Job_Type} == "FlexPepDock" ]; then
echo "
mpirun -np ${NJOBS} ${rosetta_app}/FlexPepDocking.${rosetta_version}.linuxgccrelease -database $rosetta_db -in:file:s ${input_file} -out:file:scorefile ${job_name}_score.sc -out:path:pdb ${job_name}_OUT/ -nstruct ${output_num} -ex1 -ex2aro -ignore_zero_occupancy false -score:weights ${Rosetta_score} -receptor_chain ${comp1} -flexPepDocking:peptide_chain ${comp2} -flexPepDocking:lowres_abinitio -frag3 frags/frags.3mers.offset -frag9 frags/frags.9mers.offset -flexPepDocking:frag5 frags/frags.5mers.offset -flexPepDocking:frag5_weight 0.25 -flexPepDocking:frag9_weight 0.1 -flexPepDocking:pep_refine
ls ${job_name}_OUT/ | parallel -j ${NJOBS} ${rosetta_app}/InterfaceAnalyzer.${rosetta_version}.linuxgccrelease -s ${job_name}_OUT/{} -out:file:score_only ${job_name}_Interface_Score.sc -interface ${comp1}_${comp2} -compute_packstat true -tracer_data_print false -pack_separated true -packstat::oversample 100 -add_regular_scores_to_scorefile true -pose_metrics::interface_cutoff 8.0 -sasa_calculator_probe_radius 1.4 -atomic_burial_cutoff 0.01 -no_nstruct_label true -score:weights ${Rosetta_score}
" >> ${job_name}.pbs
elif [ ${Job_Type} == "FlexPepRefine" ]; then
echo "
mpirun -np ${NJOBS} ${rosetta_app}/FlexPepDocking.${rosetta_version}.linuxgccrelease -database ${rosetta_db} -in:file:s ${input_file} -out:file:scorefile ${job_name}_score.sc -out:path:pdb ${job_name}_OUT/ -nstruct ${output_num} -ex1 -ex2aro -ignore_zero_occupancy false -score:weights ${Rosetta_score} -receptor_chain ${comp1} -flexPepDocking:peptide_chain ${comp2} -flexPepDocking:pep_refine
ls ${job_name}_OUT/ | parallel -j ${NJOBS} ${rosetta_app}/InterfaceAnalyzer.${rosetta_version}.linuxgccrelease -s ${job_name}_OUT/{} -out:file:score_only ${job_name}_Interface_Score.sc -interface "${comp1}_${comp2}" -compute_packstat true -tracer_data_print false -pack_separated true -packstat::oversample 100 -add_regular_scores_to_scorefile true -pose_metrics::interface_cutoff 8.0 -sasa_calculator_probe_radius 1.4 -atomic_burial_cutoff 0.01 -no_nstruct_label true -score:weights ${Rosetta_score}
" >> ${job_name}.pbs
elif [ ${Job_Type} == "PPI_Dock" ]; then
echo "
mpirun -np ${NJOBS} ${rosetta_app}/docking_prepack_protocol.${rosetta_version}.linuxgccrelease -docking:partners "${comp1}_${comp2}" -docking::dock_rtmin true -in:file:s ${input_file} -ex1 -ex2aro -score:weights ${Rosetta_score} -ignore_zero_occupancy false
mpirun -np ${NJOBS} ${rosetta_app}/docking_protocol.${rosetta_version}.linuxgccrelease -database ${rosetta_db} -in:file:s $(basename ${input_file%%.pdb})_0001.pdb -out:file:scorefile ${job_name}_score.sc -out:path:pdb ${job_name}_OUT/ -nstruct ${output_num} -ex1 -ex2aro -ignore_zero_occupancy false -score:weights ${Rosetta_score} -partners "${comp1}_${comp2}" -dock_pert 3 8 -randomize2 -ex1 -ex2aro -spin -use_input_sc -dock_mcm_trans_magnitude 0.7 -dock_mcm_rot_magnitude 5.0 -mh:path:scores_BB_BB ${rosetta_db}/additional_protocol_data/motif_dock/xh_16_ -mh:score:use_ss1 false -mh:score:use_ss2 false -mh:score:use_aa1 true -mh:score:use_aa2 true -docking_low_res_score motif_dock_score
ls ${job_name}_OUT/ | parallel -j ${NJOBS} ${rosetta_app}/InterfaceAnalyzer.${rosetta_version}.linuxgccrelease -s ${job_name}_OUT/{} -out:file:score_only ${job_name}_Interface_Score.sc -interface "${comp1}_${comp2}" -compute_packstat true -tracer_data_print false -pack_separated true -packstat::oversample 100 -add_regular_scores_to_scorefile true -pose_metrics::interface_cutoff 8.0 -sasa_calculator_probe_radius 1.4 -atomic_burial_cutoff 0.01 -no_nstruct_label true -score:weights ${Rosetta_score}
" >> ${job_name}.pbs
elif [ ${Job_Type} == "PPI_Refine" ]; then
echo "
mpirun -np ${NJOBS} ${rosetta_app}/docking_prepack_protocol.${rosetta_version}.linuxgccrelease -docking:partners "${comp1}_${comp2}" -docking::dock_rtmin true -in:file:s ${input_file} -ex1 -ex2aro -ignore_zero_occupancy false -score:weights ${Rosetta_score}
mpirun -np ${NJOBS} ${rosetta_app}/docking_protocol.${rosetta_version}.linuxgccrelease -database ${rosetta_db} -in:file:s $(basename ${input_file%%.pdb})_0001.pdb -out:file:scorefile ${job_name}_score.sc -out:path:pdb ${job_name}_OUT/ -nstruct ${output_num} -ex1 -ex2aro -ignore_zero_occupancy false -score:weights ${Rosetta_score} -partners "${comp1}_${comp2}" -dock_pert 3 8 -use_input_sc
ls ${job_name}_OUT/ | parallel -j ${NJOBS} ${rosetta_app}/InterfaceAnalyzer.${rosetta_version}.linuxgccrelease -s ${job_name}_OUT/{} -out:file:score_only ${job_name}_Interface_Score.sc -interface "${comp1}_${comp2}" -compute_packstat true -tracer_data_print false -pack_separated true -packstat::oversample 100 -add_regular_scores_to_scorefile true -pose_metrics::interface_cutoff 8.0 -sasa_calculator_probe_radius 1.4 -atomic_burial_cutoff 0.01 -no_nstruct_label true -score:weights ${Rosetta_score}
" >> ${job_name}.pbs
fi
else
echo "Error: must to specify only one pdb file path for docking mode!"
exit
fi
else
if [ ${MPI_mode} == "true" ];then
if [ ${Job_Type} == "Fast_Relax" ]; then
echo "
mpirun -np ${NJOBS} $rosetta_app/relax.${rosetta_version}.linuxgccrelease -database $rosetta_db -in:file:s ${input_file} -out:file:scorefile ${job_name}_score.sc -out:path:pdb ${job_name}_OUT/ -nstruct ${output_num} -ex1 -ex2aro -ignore_zero_occupancy false -score:weights ${Rosetta_score} -relax:jump_move true -relax:bb_move true -relax:chi_move true -relax:dualspace true -relax::minimize_bond_angles -relax:fast
" >> ${job_name}.pbs
elif [ ${Job_Type} == "Relax" ]; then
echo "
mpirun -np ${NJOBS} $rosetta_app/relax.${rosetta_version}.linuxgccrelease -database $rosetta_db -in:file:s ${input_file} -out:file:scorefile ${job_name}_score.sc -out:path:pdb ${job_name}_OUT/ -nstruct ${output_num} -ex1 -ex2aro -ignore_zero_occupancy false -score:weights ${Rosetta_score} -relax:jump_move true -relax:bb_move true -relax:chi_move true -relax:dualspace true -relax::minimize_bond_angles -relax:thorough
" >> ${job_name}.pbs
elif [ ${Job_Type} == "PPI_Relax" ]; then
echo "
mpirun -np ${NJOBS} $rosetta_app/relax.${rosetta_version}.linuxgccrelease -database $rosetta_db -in:file:s ${input_file} -out:file:scorefile ${job_name}_score.sc -out:path:pdb ${job_name}_OUT/ -nstruct ${output_num} -ex1 -ex2aro -ignore_zero_occupancy false -score:weights ${Rosetta_score} -relax:jump_move true -relax:bb_move true -relax:chi_move true -relax:dualspace true -relax::minimize_bond_angles -relax:script InterfaceRelax2019
" >> ${job_name}.pbs
fi
else
if [ ${Job_Type} == "Fast_Relax" ]; then
echo "
cat ${job_name}_input.list | parallel -j ${NJOBS} $rosetta_app/relax.${rosetta_version}.linuxgccrelease -database $rosetta_db -in:file:s {} -out:file:scorefile ${job_name}_score.sc -out:path:pdb ${job_name}_OUT/ -nstruct ${output_num} -ex1 -ex2aro -ignore_zero_occupancy false -score:weights ${Rosetta_score} -relax:jump_move true -relax:bb_move true -relax:chi_move true -relax:dualspace true -relax::minimize_bond_angles -relax:fast
" >> ${job_name}.pbs
elif [ ${Job_Type} == "Relax" ]; then
echo "
cat ${job_name}_input.list | parallel -j ${NJOBS} $rosetta_app/relax.${rosetta_version}.linuxgccrelease -database $rosetta_db -in:file:s {} -out:file:scorefile ${job_name}_score.sc -out:path:pdb ${job_name}_OUT/ -nstruct ${output_num} -ex1 -ex2aro -ignore_zero_occupancy false -score:weights ${Rosetta_score} -relax:jump_move true -relax:bb_move true -relax:chi_move true -relax:dualspace true -relax::minimize_bond_angles -relax:thorough
" >> ${job_name}.pbs
elif [ ${Job_Type} == "PPI_Relax" ]; then
echo "
cat ${job_name}_input.list | parallel -j ${NJOBS} $rosetta_app/relax.${rosetta_version}.linuxgccrelease -database $rosetta_db -in:file:s {} -out:file:scorefile ${job_name}_score.sc -out:path:pdb ${job_name}_OUT/ -nstruct ${output_num} -ex1 -ex2aro -ignore_zero_occupancy false -score:weights ${Rosetta_score} -relax:jump_move true -relax:bb_move true -relax:chi_move true -relax:dualspace true -relax::minimize_bond_angles -relax:script InterfaceRelax2019
" >> ${job_name}.pbs
fi
fi
fi
qsub ${job_name}.pbs
}
if [ ${Job_Type} == "Normal" ]; then
Job_Type="Normal"
PrimeMC
elif [ ${Job_Type} == "Lysozyme" ]; then
Job_Type="Lysozyme"
PrimeMC
elif [ ${Job_Type} == "MC" ]; then
Job_Type="MC"
PrimeMC
elif [ ${Job_Type} == "PPI_MMGBSA" ]; then
Job_Type="PPI_MMGBSA"
PrimeMC
elif [ ${Job_Type} == "SIDE_PRED" ]; then
Job_Type="SIDE_PRED"
backbone_sampling="yes"
PrimeMC
elif [ ${Job_Type} == "SIDE_OPT" ]; then
Job_Type="SIDE_PRED"
backbone_sampling="no"
PrimeMC
elif [ ${Job_Type} == "Fast_Relax" ] || [ ${Job_Type} == "PPI_Relax" ] || [ ${Job_Type} == "Relax" ] || [ ${Job_Type} == "FlexPepDock" ] || [ ${Job_Type} == "FlexPepRefine" ] || [ ${Job_Type} == "PPI_Dock" ] || [ ${Job_Type} == "PPI_Refine" ]; then
RosettaMC
else
echo "Error: Unknown Option: ${Job_Type}"
fi