MD.README

#!/usr/bin/sh


#Add or check to make sure that you have the necessary lines in your .bashrc file and 
#remember to logout and log back in because sometimes source .bashrc does not work effectively

vi ~/.bashrc
#-------------------------------------------------------------
module load anaconda/2
module load cuda75/toolkit/7.5.18
export CUDA_HOME="/cm/shared/apps/cuda75/toolkit/7.5.18"
export PATH=$CUDA_HOME/bin:$PATH

export AMBERHOME=/zzz.programs/amber16
export PATH=$AMBERHOME/bin\:$PATH
test -f /zzz.programs/amber16/amber.sh && source /zzz.programs/amber16/amber.sh


# STEP1
#-------------------------------------------------------------
cd 000.parameters
# Parameterize the ligand
# the only thing that needs to be changed is the mol2 file's and the number after the -nc flag 
#-nc stands for net charge 
antechamber -i ../zzz.master/system.lig.clean.mol2 -fi mol2 -o system_lig.am1bcc.mol2 -fo mol2 -at gaff -c bcc -rn LIG -nc 1

# Check for missing FF parameters
parmchk2 -i system_lig.am1bcc.mol2 -f mol2 -o system_lig.am1bcc.frcmod
#-------------------------------------------------------------

#STEP2
#-------------------------------------------------------------
cd 001.tleap_build
# Create Amber toplogy and coordinates files for the MD simulation
tleap -f tleap.build.in
# Afterwards check your leap.log for words like FATAL or ERROR thats bad
# Visualize the topology files before running MD on herbie!!!! :)
#-------------------------------------------------------------

#STEP3
#-------------------------------------------------------------
cd 002.equilibration
# Equilibrate the biological system: slowly relax them with restraints and varying temperatures
nohup bash md.equilibration.sh &

# to check your job and that its running on the nvidia gpu cards
# put the command watch infront if you want a running clock controlC to cancel it
nvidia-smi

# Submit the production job
cd 003.production/001.restrained
nohup bash  prod.sh &

# check job same as above
#-------------------------------------------------------------

#STEP4
#actually process the data to make a pretty graph
# there's a readme file in that directory
#-------------------------------------------------------------
#Post-process the trajectory
cd 004.analysis/001.rmsd
cd 004.analysis/002.hbond
#-------------------------------------------------------------