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run-GaMD-analysis.sh
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run-GaMD-analysis.sh
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#!/bin/bash
echo "
#####################################################################
# GLOW version 1.0 #
# GLOW - GaMD, Deep Learning, Free Energy Profiling Workflow #
# Authors: Hung Do, Jinan Wang, Apurba Bhattarai, Yinglong Miao #
# Update in 10/2021 #
#===================================================================#
If you use any parts of GLOW, please cite: #
Do, H., Wang, J., Bhattarai, A., and Miao, Y. (2021). GLOW - a #
Workflow Integrating Gaussian accelerated Molecular Dynamics #
and Deep Learning for Free Energy Profiling. #
#####################################################################"
echo "
=====================================================================
IMPORTANT NOTES FOR USERS:
The input file must be named: GLOW.in
In GLOW.in, please keep the format of the variables as follows,
in case you have more systems, i.e.
- workfolder_1, workfolder_2, workfolder_3, ...
- parm_sys_1, parm_sys_2, parm_sys_3, ...
- nb_prot_1, nb_prot_2, nb_prot_3, ...
- ...
Please use CTRL + A & CTRL + D to log off your terminal!
If you run into any issues, please contact [email protected]
====================================================================="
parfolder=`pwd`
source $parfolder/GLOW.in
cd $parfolder
echo "Current Directory: $parfolder"
nb_systems=$nb_systems
echo "Number of systems: $nb_systems"
echo "
#####################################################################
# (I) GaMD - Gaussian accelerated Molecular Dynamics! #
#####################################################################"
echo "Set up your system with CHARMM-GUI and run the cMD beforehand!"
source $AMBER/amber.sh
echo "
=====================================================================
# Part 1.2: Analysis of GaMD Trajectories! #
====================================================================="
for i in `seq 1 $nb_systems`
do
workfolder=workfolder_$i
parm_system=parm_sys_$i
pdb_sys=pdb_sys_$i
rst_sys=rst_sys_$i
rst_full=${!rst_sys}
pdb_full=${!pdb_sys}
nb_protein=nb_prot_$i
parm_protein=parm_prot_$i
pdb_protein=pdb_prot_$i
residues=res_idx_$i
parm_contact_map=parm_cmap_$i
pdb_contact_map=pdb_cmap_$i
trajectory_cmap=traj_cmap_$i
work_dir=${!workfolder}
parm_sys=${!parm_system}
nb_prot=${!nb_protein}
parm_prot=${!parm_protein}
pdb_prot=${!pdb_protein}
res_idx=${!residues}
parm_cmap=${!parm_contact_map}
pdb_cmap=${!pdb_contact_map}
traj_cmap=${!trajectory_cmap}
echo "The directory for system $i is $work_dir"
mkdir -p $work_dir
cat $work_dir/gamd-2.log >> $work_dir/gamd-all.log
rm ${work_dir}/extract-pdb-sys.in
echo "parm ${work_dir}/${parm_sys}
trajin ${work_dir}/${rst_full}
trajout ${work_dir}/$pdb_full"> ${work_dir}/extract-pdb-sys.in
cpptraj -i ${work_dir}/extract-pdb-sys.in
rm ${work_dir}/extract-pdb-protein.in
echo "parm ${work_dir}/${parm_sys}
trajin ${work_dir}/${rst_full}
strip !@1-${nb_prot}
trajout ${work_dir}/${pdb_prot}"> ${work_dir}/extract-pdb-protein.in
cpptraj -i ${work_dir}/extract-pdb-protein.in
rm $work_dir/extract-parm-protein.in
echo "parm $work_dir/$parm_sys
parmstrip !@1-$nb_prot
parmwrite out $work_dir/$parm_prot nochamber" >> $work_dir/extract-parm-protein.in
cpptraj -i $work_dir/extract-parm-protein.in
rm $work_dir/extract-parm-cmap.in
echo "parm $work_dir/$parm_prot
parmstrip !:$res_idx
parmstrip @H*
parmwrite out $work_dir/$parm_cmap nochamber" >> $work_dir/extract-parm-cmap.in
cpptraj -i $work_dir/extract-parm-cmap.in
rm $work_dir/extract-traj-cmap.in
echo "parm $work_dir/$parm_prot
trajin $work_dir/md-2.nc 1 last ${stride}
reference $work_dir/$pdb_prot
autoimage
rms reference mass out $work_dir/rmsd-CA.dat @CA
strip !:$res_idx
strip @H*
trajout $work_dir/$traj_cmap" >> $work_dir/extract-traj-cmap.in
cpptraj -i $work_dir/extract-traj-cmap.in
rm $work_dir/extract-pdb-cmap.in
echo "parm $work_dir/$parm_cmap
trajin $work_dir/$traj_cmap 1 1
trajout $work_dir/$pdb_cmap" >> $work_dir/extract-pdb-cmap.in
if [ $i -lt $nb_systems ]
then
cpptraj -i $work_dir/extract-pdb-cmap.in &
else
cpptraj -i $work_dir/extract-pdb-cmap.in
fi
if [ $? != 0 ]; then
echo "Errors with the analysis of GaMD simulations!"
exit 0
fi
done
echo "The analysis of GaMD production trajectories are finished!"