Difference between revisions of "2018 AMBER tutorial with 2nnq"

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−
2nnq
+
2nnq with an explicit solvent model
  
 
= Prepare the files =
 
= Prepare the files =
Line 10: Line 10:
  
 
= Parameters =
 
= Parameters =
 +
 +
The system we are working on has two main components (Protein receptor & ligand). The usual forcefield "ff14SB" contains all the parameters needed for calculations of the protein. However, the ligand is a non-protein component. Therefore, ff14SB forcefield does not contain the parameters needed for the calculations regarding the ligand.
 +
Therefore, we need to generate parameters needed for the ligand. The following steps will be taken using antechamber in order to generate the ligand parameters.
  
 
Move into 000.programs
 
Move into 000.programs
  
 
Paramaterize the ligand
 
Paramaterize the ligand
−
  antechamber -i ../zzz.master/2nnq.lig.withH.charged.pdb -fi pdb -o 2nnq_lig.am1bcc.mol2 -fo mol2 -at gaff2 -c bcc -rn LIG -nc 1
+
  antechamber -i ../zzz.master/2nnq.lig.withH.charged.pdb -fi pdb -o 2nnq_lig.am1bcc.mol2 -fo mol2 -at gaff2 -c bcc -rn LIG -nc -1
  
 
Check for missing force field parameters
 
Check for missing force field parameters
 
   
 
   
 
  parmchk2 -i 2nnq_lig.am1bcc.mol2 -f mol2 -o 2nnq_lig.am1bcc.frcmod
 
  parmchk2 -i 2nnq_lig.am1bcc.mol2 -f mol2 -o 2nnq_lig.am1bcc.frcmod
 +
 +
= TLeap =
 +
 +
Move into 001.tleap_build
 +
 +
Create tleap.build.in file
 +
 +
#!/usr/bin/sh
 +
 +
###Load Protein force field                                                   
 +
source leaprc.protein.ff14SB
 +
###Load GAFF force field (for our ligand)                                     
 +
source leaprc.gaff
 +
###Load TIP3P (water) force field                                             
 +
source leaprc.water.tip3p
 +
####Load Ions frcmod for the tip3p model                                       
 +
loadamberparams frcmod.ionsjc_tip3p
 +
###Needed so we can use igb=8 model                                           
 +
set default PBradii mbondi3
 +
 +
###Load Protein pdb file                                                       
 +
rec=loadpdb ../zzz.master/2nnq.rec.withH.charged.pdb
 +
 +
###Load Ligand frcmod/mol2                                                     
 +
loadamberparams ../000.parameters/2nnq_lig.am1bcc.frcmod
 +
lig=loadmol2 ../000.parameters/2nnq_lig.am1bcc.mol2
 +
 +
###Create gas-phase complex                                                   
 +
gascomplex= combine {rec lig}
 +
 +
###Write gas-phase pdb                                                         
 +
savepdb gascomplex 2nnq.gas.complex.pdb
 +
 +
###Write gas-phase toplogy and coord files for MMGBSA calc                     
 +
saveamberparm gascomplex 2nnq.gas.complex.prmtop 2nnq.gas.complex.rst7
 +
saveamberparm rec 2nnq.gas.receptor.prmtop 2nnq.gas.receptor.rst7
 +
saveamberparm lig 2nnq.gas.ligand.prmtop 2nnq.gas.ligand.rst7
 +
 +
###Create solvated complex (albeit redundant)                                 
 +
solvcomplex= combine {rec lig}
 +
 +
###Solvate the system                                                         
 +
solvateoct solvcomplex TIP3PBOX 12.0
 +
 +
###Neutralize system (it will add either Na or Cl depending on net charge)     
 +
addions solvcomplex Cl- 0
 +
addions solvcomplex Na+ 0
 +
 +
###Write solvated pdb file
 +
 +
###Create solvated complex (albeit redundant)                                 
 +
solvcomplex= combine {rec lig}
 +
 +
###Solvate the system                                                         
 +
solvateoct solvcomplex TIP3PBOX 12.0
 +
 +
###Neutralize system (it will add either Na or Cl depending on net charge)     
 +
addions solvcomplex Cl- 0
 +
addions solvcomplex Na+ 0
 +
 +
###Write solvated pdb file           
 +
 +
Create Amber topology and coordinates files for the MD simulation
 +
 +
tleap -f tleap.build.in
 +
 +
= Equilibration =
 +
 +
Create the following input files for the equilibration of the system.
 +
vim 01.min.mdin
 +
 +
Minmize all the hydrogens
 +
&cntrl
 +
  imin=1,          ! Minimize the initial structure
 +
  maxcyc=5000,    ! Maximum number of cycles for minimization
 +
  ntb=1,            ! Constant volume
 +
  ntp=0,            ! No pressure scaling
 +
  ntf=1,            ! Complete force evaluation
 +
  ntwx= 1000,      ! Write to trajectory file every ntwx steps
 +
  ntpr= 1000,      ! Print to mdout every ntpr steps
 +
  ntwr= 1000,      ! Write a restart file every ntwr steps
 +
  cut=  8.0,        ! Nonbonded cutoff in Angstroms
 +
  ntr=1,            ! Turn on restraints
 +
  restraintmask=":1-131 & !@H=", ! atoms to be restrained
 +
  restraint_wt=5.0, ! force constant for restraint
 +
  ntxo=1,          ! Write coordinate file in ASCII format
 +
  ioutfm=0,        ! Write trajectory file in ASCII format
 +
/
 +
 +
vim 02.equil.mdin
 +
 +
  MD simualation
 +
&cntrl
 +
  imin=0,          ! Perform MD
 +
  nstlim=50000      ! Number of MD steps
 +
  ntb=2,            ! Constant Pressure
 +
  ntc=1,            ! No SHAKE on bonds between hydrogens
 +
  dt=0.001,        ! Timestep (ps)
 +
  ntp=1,            ! Isotropic pressure scaling
 +
  barostat=1        ! Berendsen
 +
  taup=0.5          ! Pressure relaxtion time (ps)
 +
  ntf=1,            ! Complete force evaluation
 +
  ntt=3,            ! Langevin thermostat
 +
  gamma_ln=2.0      ! Collision Frequency for thermostat
 +
  ig=-1,            ! Random seed for thermostat
 +
  temp0=298.15      ! Simulation temperature (K)
 +
  ntwx= 1000,      ! Write to trajectory file every ntwx steps
 +
  ntpr= 1000,      ! Print to mdout every ntpr steps
 +
  ntwr= 1000,      ! Write a restart file every ntwr steps
 +
  cut=  8.0,        ! Nonbonded cutoff in Angstroms
 +
  ntr=1,            ! Turn on restraints
 +
  restraintmask=":1-131 & !@H=", ! atoms to be restrained
 +
  restraint_wt=5.0, ! force constant for restraint
 +
  ntxo=1,          ! Write coordinate file in ASCII format
 +
  ioutfm=0,        ! Write trajectory file in ASCII format
 +
  iwrap=1,          ! iwrap is turned on
 +
/
 +
 +
vim 03.min.mdin
 +
 +
Minmize all the hydrogens
 +
&cntrl
 +
  imin=1,          ! Minimize the initial structure
 +
  maxcyc=1000,    ! Maximum number of cycles for minimization
 +
  ntb=1,            ! Constant volume
 +
  ntp=0,            ! No pressure scaling
 +
  ntf=1,            ! Complete force evaluation
 +
  ntwx= 1000,      ! Write to trajectory file every ntwx steps
 +
  ntpr= 1000,      ! Print to mdout every ntpr steps
 +
  ntwr= 1000,      ! Write a restart file every ntwr steps
 +
  cut=  8.0,        ! Nonbonded cutoff in Angstroms
 +
  ntr=1,            ! Turn on restraints
 +
  restraintmask=":1-131 & !@H=", ! atoms to be restrained
 +
  restraint_wt=2.0, ! force constant for restraint
 +
  ntxo=1,          ! Write coordinate file in ASCII format
 +
  ioutfm=0,        ! Write trajectory file in ASCII format
 +
/
 +
 +
vim 04.min.mdin
 +
 +
  Minmize all the hydrogens
 +
&cntrl
 +
  imin=1,          ! Minimize the initial structure
 +
  maxcyc=1000,    ! Maximum number of cycles for minimization
 +
  ntb=1,            ! Constant volume
 +
  ntp=0,            ! No pressure scaling
 +
  ntf=1,            ! Complete force evaluation
 +
  ntwx= 1000,      ! Write to trajectory file every ntwx steps
 +
  ntpr= 1000,      ! Print to mdout every ntpr steps
 +
  ntwr= 1000,      ! Write a restart file every ntwr steps
 +
  cut=  8.0,        ! Nonbonded cutoff in Angstroms
 +
  ntr=1,            ! Turn on restraints
 +
  restraintmask=":1-131 & !@H=", ! atoms to be restrained
 +
  restraint_wt=0.1, ! force constant for restraint
 +
  ntxo=1,          ! Write coordinate file in ASCII format
 +
  ioutfm=0,        ! Write trajectory file in ASCII format
 +
/
 +
 +
vim 05.min.mdin
 +
 +
  Minmize all the hydrogens
 +
&cntrl
 +
  imin=1,          ! Minimize the initial structure
 +
  maxcyc=1000,    ! Maximum number of cycles for minimization
 +
  ntb=1,            ! Constant volume
 +
  ntp=0,            ! No pressure scaling
 +
  ntf=1,            ! Complete force evaluation
 +
  ntwx= 1000,      ! Write to trajectory file every ntwx steps
 +
  ntpr= 1000,      ! Print to mdout every ntpr steps
 +
  ntwr= 1000,      ! Write a restart file every ntwr steps
 +
  cut=  8.0,        ! Nonbonded cutoff in Angstroms
 +
  ntr=1,            ! Turn on restraints
 +
  restraintmask=":1-131 & !@H=", ! atoms to be restrained
 +
  restraint_wt=0.05, ! force constant for restraint
 +
  ntxo=1,          ! Write coordinate file in ASCII format
 +
  ioutfm=0,        ! Write trajectory file in ASCII format
 +
/
 +
 +
vim 06.equil.mdin
 +
 +
  MD simualation
 +
&cntrl
 +
  imin=0,          ! Perform MD
 +
  nstlim=50000      ! Number of MD steps
 +
  ntb=2,            ! Constant Pressure
 +
  ntc=1,            ! No SHAKE on bonds between hydrogens
 +
  dt=0.001,        ! Timestep (ps)
 +
  ntp=1,            ! Isotropic pressure scaling
 +
  barostat=1        ! Berendsen
 +
  taup=0.5          ! Pressure relaxtion time (ps)
 +
  ntf=1,            ! Complete force evaluation
 +
  ntt=3,            ! Langevin thermostat
 +
  gamma_ln=2.0      ! Collision Frequency for thermostat
 +
  ig=-1,            ! Random seed for thermostat
 +
  temp0=298.15      ! Simulation temperature (K)
 +
  ntwx= 1000,      ! Write to trajectory file every ntwx steps
 +
  ntpr= 1000,      ! Print to mdout every ntpr steps
 +
  ntwr= 1000,      ! Write a restart file every ntwr steps
 +
  cut=  8.0,        ! Nonbonded cutoff in Angstroms
 +
  ntr=1,            ! Turn on restraints
 +
  restraintmask=":1-131 & !@H=", ! atoms to be restrained
 +
  restraint_wt=1.0, ! force constant for restraint
 +
  ntxo=1,          ! Write coordinate file in ASCII format
 +
  ioutfm=0,        ! Write trajectory file in ASCII format
 +
  iwrap=1,          ! iwrap is turned on
 +
/
 +
 +
vim 07.equil.mdin
 +
 +
MD simulation
 +
&cntrl
 +
  imin=0,          ! Perform MD
 +
  nstlim=50000      ! Number of MD steps
 +
  ntx=5,            ! Positions and velocities read formatted
 +
  irest=1,          ! Restart calculation
 +
  ntc=1,            ! No SHAKE on for bonds with hydrogen
 +
  dt=0.001,        ! Timestep (ps)
 +
  ntb=2,            ! Constant Pressure
 +
  ntp=1,            ! Isotropic pressure scaling
 +
  barostat=1        ! Berendsen
 +
  taup=0.5          ! Pressure relaxtion time (ps)
 +
  ntf=1,            ! Complete force evaluation
 +
  ntt=3,            ! Langevin thermostat
 +
  gamma_ln=2.0      ! Collision Frequency for thermostat
 +
  ig=-1,            ! Random seed for thermostat
 +
  temp0=298.15      ! Simulation temperature (K)
 +
  ntwx= 1000,      ! Write to trajectory file every ntwx steps
 +
  ntpr= 1000,      ! Print to mdout every ntpr steps
 +
  ntwr= 1000,      ! Write a restart file every ntwr steps
 +
  cut=  8.0,        ! Nonbonded cutoff in Angstroms
 +
  ntr=1,            ! Turn on restraints
 +
  restraintmask=":1-131 & !@H=", ! atoms to be restrained
 +
  restraint_wt=0.5, ! force constant for restraint
 +
  ntxo=1,          ! Write coordinate file in ASCII format
 +
  ioutfm=0,        ! Write trajectory file in ASCII format
 +
  iwrap=1,          ! iwrap is turned on
 +
/
 +
 +
vim 08.equil.mdin
 +
 +
MD simulations
 +
&cntrl
 +
  imin=0,          ! Perform MD
 +
  nstlim=50000      ! Number of MD steps
 +
  ntx=5,            ! Positions and velocities read formatted
 +
  irest=1,          ! Restart calculation
 +
  ntc=1,            ! No SHAKE on for bonds with hydrogen
 +
  dt=0.001,        ! Timestep (ps)
 +
  ntb=2,            ! Constant Pressure
 +
  ntp=1,            ! Isotropic pressure scaling
 +
  barostat=1        ! Berendsen
 +
  taup=0.5          ! Pressure relaxtion time (ps)
 +
  ntf=1,            ! Complete force evaluation
 +
  ntt=3,            ! Langevin thermostat
 +
  gamma_ln=2.0      ! Collision Frequency for thermostat
 +
  ig=-1,            ! Random seed for thermostat
 +
  temp0=298.15      ! Simulation temperature (K)
 +
  ntwx= 1000,      ! Write to trajectory file every ntwx steps
 +
  ntpr= 1000,      ! Print to mdout every ntpr steps
 +
  ntwr= 1000,      ! Write a restart file every ntwr steps
 +
  cut=  8.0,        ! Nonbonded cutoff in Angstroms
 +
  ntr=1,            ! Turn on restraints
 +
  restraintmask=":1-131@CA,C,N", ! atoms to be restrained
 +
  restraint_wt=0.1, ! force constant for restraint
 +
  ntxo=1,          ! Write coordinate file in ASCII format
 +
  ioutfm=0,        ! Write trajectory file in ASCII format
 +
  iwrap=1,          ! iwrap is turned on
 +
/
 +
 +
vim 09.equil.mdin
 +
 +
 +
MD simulations
 +
&cntrl
 +
  imin=0,          ! Perform MD
 +
  nstlim=50000      ! Number of MD steps
 +
  ntx=5,            ! Positions and velocities read formatted
 +
  irest=1,          ! Restart calculation
 +
  ntc=1,            ! No SHAKE on for bonds with hydrogen
 +
  dt=0.001,        ! Timestep (ps)
 +
  ntb=2,            ! Constant Pressure
 +
  ntp=1,            ! Isotropic pressure scaling
 +
  barostat=1        ! Berendsen
 +
  taup=0.5          ! Pressure relaxtion time (ps)
 +
  ntf=1,            ! Complete force evaluation
 +
  ntt=3,            ! Langevin thermostat
 +
  gamma_ln=2.0      ! Collision Frequency for thermostat
 +
  ig=-1,            ! Random seed for thermostat
 +
  temp0=298.15      ! Simulation temperature (K)
 +
  ntwx= 1000,      ! Write to trajectory file every ntwx steps
 +
  ntpr= 1000,      ! Print to mdout every ntpr steps
 +
  ntwr= 1000,      ! Write a restart file every ntwr steps
 +
  cut=  8.0,        ! Nonbonded cutoff in Angstroms
 +
  ntr=1,            ! Turn on restraints
 +
  restraintmask=":1-131@CA,C,N", ! atoms to be restrained
 +
  restraint_wt=0.1, ! force constant for restraint
 +
  ntxo=1,          ! Write coordinate file in ASCII format
 +
  ioutfm=0,        ! Write trajectory file in ASCII format
 +
  iwrap=1,          ! iwrap is turned on
 +
/
 +
 +
Create a submission script that utilizes, above input files to equilibrate the biological system.
 +
vim mdequilibration.sh
 +
 +
#!/bin/sh                                                                                                                                                                                                                                   
 +
#PBS -N 2nnq_equilibration                                                                                                                                                                                                                   
 +
#PBS -l walltime=04:00:00                                                                                                                                                                                                                   
 +
#PBS -l nodes=2:ppn=28                                                                                                                                                                                                                       
 +
#PBS -j oe                                                                                                                                                                                                                                   
 +
#PBS -q long                                                                                                                                                                                                                                 
 +
 +
cd $PBS_O_WORKDIR
 +
 +
echo "Started Equilibration on `date` "
 +
do_parallel="sander"
 +
 +
prmtop="../001.tleap_build/2nnq.wet.complex.prmtop"
 +
coords="../001.tleap_build/2nnq.wet.complex"
 +
 +
 +
MDINPUTS=(01.min 02.equil 03.min 04.min 05.min 06.equil 07.equil 08.equil 09.equil)
 +
 +
for input in ${MDINPUTS[@]}; do
 +
 +
  $do_parallel -O -i ${input}.mdin -o ${input}.mdout -p $prmtop -c ${coords}.rst7 -ref ${coords}.rst7 -x ${input}.trj -inf
 +
${input}.info -r ${input}.rst7
 +
  coords=$input
 +
done
 +
 +
echo "Finished Equilibration on `date` "
 +
 +
Submit the job
 +
 +
qsub md.equilibration.sh
 +
 +
= Production =
 +
 +
Move into 003.production
 +
 +
Move into 001.restrained
 +
 +
Create 10.prod.mdin
 +
 +
  MD simulations
 +
&cntrl
 +
  imin=0,          ! Perform MD
 +
  nstlim=5000000,  ! Number of MD steps
 +
  ntx=5,            ! Positions and velocities read formatted
 +
  irest=1,          ! Restart calculation
 +
  ntc=2,            ! SHAKE on for bonds with hydrogen
 +
  dt=0.002,        ! Timestep (ps)
 +
  ntb=2,            ! Constant Pressure
 +
  ntp=1,            ! Isotropic pressure scaling
 +
  barostat=1        ! Berendsen
 +
  taup=0.5          ! Pressure relaxtion time (ps)
 +
  ntf=2,            ! No force evaluation for bonds with hydrogen
 +
  ntt=3,            ! Langevin thermostat
 +
  gamma_ln=2.0      ! Collision Frequency for thermostat
 +
  ig=-1,            ! Random seed for thermostat
 +
  temp0=298.15      ! Simulation temperature (K)
 +
  ntwx= 2500,      ! Write to trajectory file every ntwx steps
 +
  ntpr= 2500,      ! Print to mdout every ntpr steps
 +
  ntwr= 5000000,    ! Write a restart file every ntwr steps
 +
  cut=8.0,          ! Nonbonded cutoff in Angstroms
 +
  ntr=1,            ! Turn on restraints
 +
  restraintmask=":1-287@CA,C,N", ! atoms to be restrained
 +
  restraint_wt=0.1, ! force constant for restraint
 +
  ntxo=1,          ! Write coordinate file in ASCII format
 +
  ioutfm=0,        ! Write trajectory file in ASCII format
 +
  iwrap=1,          ! iwrap is turned on
 +
 +
Create prod.sh
 +
 
 +
  #!/bin/sh                                                                                                                                                                                                                                   
 +
#PBS -N 2nnq_production                                                                                                                                                                                                                     
 +
#PBS -l walltime=24:00:00                                                                                                                                                                                                                   
 +
#PBS -l nodes=2:ppn=24                                                                                                                                                                                                                       
 +
#PBS -j oe                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
 +
#PBS -o production.output
 +
#PBS -q long                                                                                                                                                                                                                   
 +
 +
cd $PBS_O_WORKDIR
 +
 +
echo "Started Production on `date` "
 +
#do_parallel="mpirun pmemd.MPI"                                                                                                                                                                                                             
 +
do_cuda="mpirun pmemd.MPI"
 +
 +
prmtop="../../001.tleap_build/2nnq.wet.complex.prmtop"
 +
coords="../../002.equilbration/09.equil"
 +
 +
 +
MDINPUTS=(10.prod)
 +
 +
for input in ${MDINPUTS[@]}; do
 +
 +
  $do_cuda -O -i ${input}.mdin -o ${input}.mdout -p $prmtop -c ${coords}.rst7 -ref ${coords}.rst7 -x ${input}.trj -inf
 +
${input}.info -r ${input}.rst7
 +
  coords=$input
 +
done
 +
 +
echo "Finished Production on `date` "
 +
 +
 +
Submit the job
 +
qsub prod.sh
 +
 +
Move into 002.unrestrained
 +
 +
Create 10.prod.mdin
 +
 +
  MD simulations
 +
&cntrl
 +
  imin=0,          ! Perform MD
 +
  nstlim=5000000    ! Number of MD steps
 +
  ntx=5,            ! Positions and velocities read formatted
 +
  irest=1,          ! Restart calculation
 +
  ntc=2,            ! SHAKE on for bonds with hydrogen
 +
  dt=0.002,        ! Timestep (ps)
 +
  ntb=2,            ! Constant Pressure
 +
  ntp=1,            ! Isotropic pressure scaling
 +
  barostat=1        ! Berendsen
 +
  taup=0.5          ! Pressure relaxtion time (ps)
 +
  ntf=2,            ! No force evaluation for bonds with hydrogen
 +
  ntt=3,            ! Langevin thermostat
 +
  gamma_ln=2.0      ! Collision Frequency for thermostat
 +
  ig=-1,            ! Random seed for thermostat
 +
  temp0=298.15      ! Simulation temperature (K)
 +
  ntwx= 2500,      ! Write to trajectory file every ntwx steps
 +
  ntpr= 2500,      ! Print to mdout every ntpr steps
 +
  ntwr= 5000000,    ! Write a restart file every ntwr steps
 +
  cut=  8.0,        ! Nonbonded cutoff in Angstroms
 +
  ntxo=1,          ! Write coordinate file in ASCII format
 +
  ioutfm=0,        ! Write trajectory file in ASCII format
 +
  iwrap=1,          ! iwrap is turned on
 +
/
 +
 +
 +
Create prod.sh
 +
 
 +
  #!/bin/sh                                                                                                                                                                                                                                   
 +
#PBS -N 2nnq_production                                                                                                                                                                                                                     
 +
#PBS -l walltime=24:00:00                                                                                                                                                                                                                   
 +
#PBS -l nodes=2:ppn=24                                                                                                                                                                                                                       
 +
#PBS -j oe                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
 +
#PBS -o production.output
 +
#PBS -q long                                                                                                                                                                                                                   
 +
 +
cd $PBS_O_WORKDIR
 +
 +
echo "Started Production on `date` "
 +
#do_parallel="mpirun pmemd.MPI"                                                                                                                                                                                                             
 +
do_cuda="mpirun pmemd.MPI"
 +
 +
prmtop="../../001.tleap_build/2nnq.wet.complex.prmtop"
 +
coords="../../002.equilbration/09.equil"
 +
 +
 +
MDINPUTS=(10.prod)
 +
 +
for input in ${MDINPUTS[@]}; do
 +
 +
  $do_cuda -O -i ${input}.mdin -o ${input}.mdout -p $prmtop -c ${coords}.rst7 -ref ${coords}.rst7 -x ${input}.trj -inf
 +
${input}.info -r ${input}.rst7
 +
  coords=$input
 +
done
 +
 +
echo "Finished Production on `date` "
 +
 +
 +
Submit the job
 +
qsub prod.sh
 +
 +
= Analysis =
 +
 +
== RMSD ==
 +
How far our ligand moved and how far our receptor moved
 +
 +
Create cpptraj.strip.wat.in
 +
 +
#!/usr/bin/sh                                                             
 +
parm ../../001.tleap_build/2nnq.wet.complex.prmtop
 +
#read in trajectory                                                       
 +
trajin ../../003.production/001.restrained/10.prod.trj
 +
#read in reference                                                         
 +
reference ../../001.tleap_build/2nnq.wet.complex.rst7
 +
#compute rmsd and align CA to the crystal structure                       
 +
rmsd rms1 reference :1-131@CA
 +
#strip Solvent                                                             
 +
strip :WAT:Na+:Cl-
 +
#create gas-phase trajectory                                               
 +
trajout 2nnq.stripfit.restrained.gas.trj nobox
 +
 +
Run cpptraj
 +
cpptraj -i cpptraj.strip.wat.in
 +
 +
Create cpptraj.rmsd.lig.in
 +
#!/usr/bin/sh                                                             
 +
#trajin the trajectory                                                     
 +
trajin 2nnq.stripfit.restrained.gas.trj
 +
#read in the reference                                                     
 +
reference ../../001.tleap_build/2nnq.gas.complex.rst7
 +
#compute the RMSD (do not fit the internal geometries first, included rigid body motions                                                             
 +
#and convert the frames to ns (framenum*.005)                             
 +
rmsd rms1 ":132&!(@H=)" nofit mass out 2nnq.lig.restrained.rmsd.nofit.dat time .005
 +
#histogram the nofit rmsd                                                 
 +
histogram rms1,*,*,.1,* norm out 2nnq.lig.restrained.rmsd.nofit.histogram.dat
 +
 +
 +
Run cpptraj
 +
cpptraj -p ../../001.tleap_build/2nnq.gas.complex.prmtop -i cpptraj.rmsd.lig.in
 +
 +
Create cpptraj.rmsd.rec.in
 +
#!/usr/bin/sh                                                                                   
 +
#trajin the trajectory                                                                         
 +
trajin 2nnq.stripfit.restrained.gas.trj
 +
#read in the reference                                                                         
 +
reference ../../001.tleap_build/2nnq.gas.complex.rst7
 +
#compute the RMSD (do not fit the internal geometries first, included rigid body motions       
 +
#and convert the frames to ns (framenum*.005)                                                   
 +
rmsd rms1 ":1-131&!(@H=)" nofit mass out 2nnq.rec.restrained.rmsd.nofit.dat time .005
 +
#histogram the nofit rmsd                                                                       
 +
histogram rms1,*,*,.1,* norm out 2nnq.rec.restrained.rmsd.nofit.histogram.dat
 +
 +
Run cpptraj
 +
cpptraj -p ../../001.tleap_build/2nnq.gas.complex.prmtop -i cpptraj.rmsd.rec.in
 +
 +
==H Bond==
 +
Hydrogen bonding
 +
 +
Create cpptraj.hbond.in
 +
 +
#!/usr/bin/sh                                                                                                                             
 +
#read in trajectory                                                                                                                       
 +
trajin ../../003.production/001.restrained/10.prod.trj
 +
#wrap everything into one periodic cell                                                                                                   
 +
#autoimage                                                                                                                               
 +
#compute intra and water mediated hydrogen bonds                                                                                         
 +
hbond hb1 :1-288 out 2nnq_sunitinib.hbond.out avgout 2nnq_sunitinib.hbond.avg.dat solventdonor :WAT solventacceptor :WAT@O
 +
nointramol brid\
 +
geout 2nnq_sunitinib.bridge-water.dat dist 3.0 angle 140
 +
 +
Run cpptraj
 +
 +
cpptraj -p ../../001.tleap_build/2nnq.wet.complex.prmtop -i cpptraj.hbond.in
 +
 +
==MMGBSA==
 +
This will analyze how strongly our small molecule binds to our receptor.
 +
 +
Create mmgbsa.in
 +
 +
mmgbsa 2nnq analysis                                                                                                                   
 +
&general                                                                                                                                 
 +
  interval=1, netcdf=1,                                                                                                                   
 +
  keep_files=0,                                                                                                                           
 +
                                                                                                                                           
 +
/                                                                                                                                         
 +
&gb                                                                                                                                       
 +
  igb=8,                                                                                                                                 
 +
  saltcon=0.0, surften=0.0072,                                                                                                           
 +
  surfoff=0.0, molsurf=0,                                                                                                                 
 +
/                                                                                                                                         
 +
&nmode                                                                                                                                   
 +
  drms=0.001, maxcyc=10000,                                                                                                               
 +
  nminterval=250, nmendframe=2000,                                                                                                       
 +
  nmode_igb=1,                                                                                                                             
 +
/                                                                                                                                         
 +
 +
 +
Create mmgbsa.sh
 +
 +
#!/bin/bash                                                                                                                               
 +
#PBS -l walltime=35:00:00                                                                                                                 
 +
#PBS -l nodes=1:ppn=24                                                                                                                   
 +
#PBS -N 4qmz_mmgbsa                                                                                                                       
 +
#PBS -V                                                                                                                                   
 +
#PBS -j oe                                                                                                                               
 +
#PBS -q long-24core                                                                                                                       
 +
 +
cd $PBS_O_WORKDIR
 +
 +
#Define topology files                                                                                                                   
 +
solv_prmtop="../../001.tleap_build/2nnq.wet.complex.prmtop"
 +
complex_prmtop="../../001.tleap_build/2nnq.gas.complex.prmtop"
 +
receptor_prmtop="../../001.tleap_build/2nnq.gas.receptor.prmtop"
 +
ligand_prmtop="../../001.tleap_build/2nnq.gas.ligand.prmtop"
 +
trajectory="../../003.production/001.restrained/10.prod.trj"
 +
 
 +
 +
#create mmgbsa input file                                                                                                                 
 +
cat >mmgbsa.in<<EOF                                                                                                                       
 +
mmgbsa HIVgp41 analysis                                                                                                                   
 +
&general                                                                                                                                 
 +
  interval=1, netcdf=1,                                                                                                                   
 +
  keep_files=0,                                                                                                                           
 +
                                                                                                                                           
 +
/                                                                                                                                         
 +
&gb                                                                                                                                       
 +
  igb=8,                                                                                                                                 
 +
  saltcon=0.0, surften=0.0072,                                                                                                           
 +
  surfoff=0.0, molsurf=0,                                                                                                                 
 +
/                                                                                                                                         
 +
&nmode                                                                                                                                   
 +
  drms=0.001, maxcyc=10000,                                                                                                               
 +
  nminterval=250, nmendframe=2000,                                                                                                       
 +
  nmode_igb=1,                                                                                                                           
 +
/                                                                                                                                         
 +
EOF                                                                                                                                       
 +
 
 +
 +
 
 +
 +
MMPBSA.py -O -i mmgbsa.in \
 +
            -o  2nnq.mmgbsa.results.dat \
 +
            -eo 2nnq.mmgbsa.per-frame.dat \
 +
            -sp ${solv_prmtop} \
 +
            -cp ${complex_prmtop} \
 +
            -rp ${receptor_prmtop} \
 +
            -lp ${ligand_prmtop} \
 +
            -y ${trajectory}
 +
 +
 +
Submit your script
 +
 +
qsub mmgbsa.sh
 +
 +
The last line of our 2nnq.mmgbsa.results.dat file shows that our delta G binding is -24.4431 +/-  5.4851.

Latest revision as of 20:39, 2 April 2019

2nnq with an explicit solvent model

Prepare the files

Convert 2nnq.lig.withH.charged.mol2 to pdb in chimera

Convert 2nnq.rec.withH.charged.mol2 to pdb in chimera

Copy into zzz.master

Parameters

The system we are working on has two main components (Protein receptor & ligand). The usual forcefield "ff14SB" contains all the parameters needed for calculations of the protein. However, the ligand is a non-protein component. Therefore, ff14SB forcefield does not contain the parameters needed for the calculations regarding the ligand. Therefore, we need to generate parameters needed for the ligand. The following steps will be taken using antechamber in order to generate the ligand parameters.

Move into 000.programs

Paramaterize the ligand 

antechamber -i ../zzz.master/2nnq.lig.withH.charged.pdb -fi pdb -o 2nnq_lig.am1bcc.mol2 -fo mol2 -at gaff2 -c bcc -rn LIG -nc -1

Check for missing force field parameters 

parmchk2 -i 2nnq_lig.am1bcc.mol2 -f mol2 -o 2nnq_lig.am1bcc.frcmod

TLeap

Move into 001.tleap_build

Create tleap.build.in file 

#!/usr/bin/sh

###Load Protein force field                                                     
source leaprc.protein.ff14SB
###Load GAFF force field (for our ligand)                                       
source leaprc.gaff
###Load TIP3P (water) force field                                               
source leaprc.water.tip3p
####Load Ions frcmod for the tip3p model                                        
loadamberparams frcmod.ionsjc_tip3p
###Needed so we can use igb=8 model                                             
set default PBradii mbondi3

###Load Protein pdb file                                                        
rec=loadpdb ../zzz.master/2nnq.rec.withH.charged.pdb

###Load Ligand frcmod/mol2                                                      
loadamberparams ../000.parameters/2nnq_lig.am1bcc.frcmod
lig=loadmol2 ../000.parameters/2nnq_lig.am1bcc.mol2

###Create gas-phase complex                                                     
gascomplex= combine {rec lig}

###Write gas-phase pdb                                                          
savepdb gascomplex 2nnq.gas.complex.pdb

###Write gas-phase toplogy and coord files for MMGBSA calc                      
saveamberparm gascomplex 2nnq.gas.complex.prmtop 2nnq.gas.complex.rst7
saveamberparm rec 2nnq.gas.receptor.prmtop 2nnq.gas.receptor.rst7
saveamberparm lig 2nnq.gas.ligand.prmtop 2nnq.gas.ligand.rst7

###Create solvated complex (albeit redundant)                                   
solvcomplex= combine {rec lig}

###Solvate the system                                                           
solvateoct solvcomplex TIP3PBOX 12.0

###Neutralize system (it will add either Na or Cl depending on net charge)      
addions solvcomplex Cl- 0
addions solvcomplex Na+ 0

###Write solvated pdb file

###Create solvated complex (albeit redundant)                                   
solvcomplex= combine {rec lig}

###Solvate the system                                                           
solvateoct solvcomplex TIP3PBOX 12.0

###Neutralize system (it will add either Na or Cl depending on net charge)      
addions solvcomplex Cl- 0
addions solvcomplex Na+ 0

###Write solvated pdb file

Create Amber topology and coordinates files for the MD simulation 

tleap -f tleap.build.in

Equilibration

Create the following input files for the equilibration of the system. 

vim 01.min.mdin

Minmize all the hydrogens
&cntrl
 imin=1,           ! Minimize the initial structure
 maxcyc=5000,    ! Maximum number of cycles for minimization
 ntb=1,            ! Constant volume
 ntp=0,            ! No pressure scaling
 ntf=1,            ! Complete force evaluation
 ntwx= 1000,       ! Write to trajectory file every ntwx steps
 ntpr= 1000,       ! Print to mdout every ntpr steps
 ntwr= 1000,       ! Write a restart file every ntwr steps
 cut=  8.0,        ! Nonbonded cutoff in Angstroms
 ntr=1,            ! Turn on restraints
 restraintmask=":1-131 & !@H=", ! atoms to be restrained
 restraint_wt=5.0, ! force constant for restraint
 ntxo=1,           ! Write coordinate file in ASCII format
 ioutfm=0,         ! Write trajectory file in ASCII format
/

vim 02.equil.mdin

 MD simualation
&cntrl
 imin=0,           ! Perform MD
 nstlim=50000      ! Number of MD steps
 ntb=2,            ! Constant Pressure
 ntc=1,            ! No SHAKE on bonds between hydrogens
 dt=0.001,         ! Timestep (ps)
 ntp=1,            ! Isotropic pressure scaling
 barostat=1        ! Berendsen
 taup=0.5          ! Pressure relaxtion time (ps)
 ntf=1,            ! Complete force evaluation
 ntt=3,            ! Langevin thermostat
 gamma_ln=2.0      ! Collision Frequency for thermostat
 ig=-1,            ! Random seed for thermostat
 temp0=298.15      ! Simulation temperature (K)
 ntwx= 1000,       ! Write to trajectory file every ntwx steps
 ntpr= 1000,       ! Print to mdout every ntpr steps
 ntwr= 1000,       ! Write a restart file every ntwr steps
 cut=  8.0,        ! Nonbonded cutoff in Angstroms
 ntr=1,            ! Turn on restraints
 restraintmask=":1-131 & !@H=", ! atoms to be restrained
 restraint_wt=5.0, ! force constant for restraint
 ntxo=1,           ! Write coordinate file in ASCII format
 ioutfm=0,         ! Write trajectory file in ASCII format
 iwrap=1,          ! iwrap is turned on
/

vim 03.min.mdin

Minmize all the hydrogens
&cntrl
 imin=1,           ! Minimize the initial structure
 maxcyc=1000,    ! Maximum number of cycles for minimization
 ntb=1,            ! Constant volume
 ntp=0,            ! No pressure scaling
 ntf=1,            ! Complete force evaluation
 ntwx= 1000,       ! Write to trajectory file every ntwx steps
 ntpr= 1000,       ! Print to mdout every ntpr steps
 ntwr= 1000,       ! Write a restart file every ntwr steps
 cut=  8.0,        ! Nonbonded cutoff in Angstroms
 ntr=1,            ! Turn on restraints
 restraintmask=":1-131 & !@H=", ! atoms to be restrained
 restraint_wt=2.0, ! force constant for restraint
 ntxo=1,           ! Write coordinate file in ASCII format
 ioutfm=0,         ! Write trajectory file in ASCII format
/

vim 04.min.mdin

 Minmize all the hydrogens
&cntrl
 imin=1,           ! Minimize the initial structure
 maxcyc=1000,    ! Maximum number of cycles for minimization
 ntb=1,            ! Constant volume
 ntp=0,            ! No pressure scaling
 ntf=1,            ! Complete force evaluation
 ntwx= 1000,       ! Write to trajectory file every ntwx steps
 ntpr= 1000,       ! Print to mdout every ntpr steps
 ntwr= 1000,       ! Write a restart file every ntwr steps
 cut=  8.0,        ! Nonbonded cutoff in Angstroms
 ntr=1,            ! Turn on restraints
 restraintmask=":1-131 & !@H=", ! atoms to be restrained
 restraint_wt=0.1, ! force constant for restraint
 ntxo=1,           ! Write coordinate file in ASCII format
 ioutfm=0,         ! Write trajectory file in ASCII format
/

vim 05.min.mdin

  Minmize all the hydrogens
&cntrl
 imin=1,           ! Minimize the initial structure
 maxcyc=1000,    ! Maximum number of cycles for minimization
 ntb=1,            ! Constant volume
 ntp=0,            ! No pressure scaling
 ntf=1,            ! Complete force evaluation
 ntwx= 1000,       ! Write to trajectory file every ntwx steps
 ntpr= 1000,       ! Print to mdout every ntpr steps
 ntwr= 1000,       ! Write a restart file every ntwr steps
 cut=  8.0,        ! Nonbonded cutoff in Angstroms
 ntr=1,            ! Turn on restraints
 restraintmask=":1-131 & !@H=", ! atoms to be restrained
 restraint_wt=0.05, ! force constant for restraint
 ntxo=1,           ! Write coordinate file in ASCII format
 ioutfm=0,         ! Write trajectory file in ASCII format
/

vim 06.equil.mdin

 MD simualation
&cntrl
 imin=0,           ! Perform MD
 nstlim=50000      ! Number of MD steps
 ntb=2,            ! Constant Pressure
 ntc=1,            ! No SHAKE on bonds between hydrogens
 dt=0.001,         ! Timestep (ps)
 ntp=1,            ! Isotropic pressure scaling
 barostat=1        ! Berendsen
 taup=0.5          ! Pressure relaxtion time (ps)
 ntf=1,            ! Complete force evaluation
 ntt=3,            ! Langevin thermostat
 gamma_ln=2.0      ! Collision Frequency for thermostat
 ig=-1,            ! Random seed for thermostat
 temp0=298.15      ! Simulation temperature (K)
 ntwx= 1000,       ! Write to trajectory file every ntwx steps
 ntpr= 1000,       ! Print to mdout every ntpr steps
 ntwr= 1000,       ! Write a restart file every ntwr steps
 cut=  8.0,        ! Nonbonded cutoff in Angstroms
 ntr=1,            ! Turn on restraints
 restraintmask=":1-131 & !@H=", ! atoms to be restrained
 restraint_wt=1.0, ! force constant for restraint
 ntxo=1,           ! Write coordinate file in ASCII format
 ioutfm=0,         ! Write trajectory file in ASCII format
 iwrap=1,          ! iwrap is turned on
/

vim 07.equil.mdin

MD simulation
&cntrl
 imin=0,           ! Perform MD
 nstlim=50000      ! Number of MD steps
 ntx=5,            ! Positions and velocities read formatted
 irest=1,          ! Restart calculation
 ntc=1,            ! No SHAKE on for bonds with hydrogen
 dt=0.001,         ! Timestep (ps)
 ntb=2,            ! Constant Pressure
 ntp=1,            ! Isotropic pressure scaling
 barostat=1        ! Berendsen
 taup=0.5          ! Pressure relaxtion time (ps)
 ntf=1,            ! Complete force evaluation
 ntt=3,            ! Langevin thermostat
 gamma_ln=2.0      ! Collision Frequency for thermostat
 ig=-1,            ! Random seed for thermostat
 temp0=298.15      ! Simulation temperature (K)
 ntwx= 1000,       ! Write to trajectory file every ntwx steps
 ntpr= 1000,       ! Print to mdout every ntpr steps
 ntwr= 1000,       ! Write a restart file every ntwr steps
 cut=  8.0,        ! Nonbonded cutoff in Angstroms
 ntr=1,            ! Turn on restraints
 restraintmask=":1-131 & !@H=", ! atoms to be restrained
 restraint_wt=0.5, ! force constant for restraint
 ntxo=1,           ! Write coordinate file in ASCII format
 ioutfm=0,         ! Write trajectory file in ASCII format
 iwrap=1,          ! iwrap is turned on
/

vim 08.equil.mdin

MD simulations
&cntrl
 imin=0,           ! Perform MD
 nstlim=50000      ! Number of MD steps
 ntx=5,            ! Positions and velocities read formatted
 irest=1,          ! Restart calculation
 ntc=1,            ! No SHAKE on for bonds with hydrogen
 dt=0.001,         ! Timestep (ps)
 ntb=2,            ! Constant Pressure
 ntp=1,            ! Isotropic pressure scaling
 barostat=1        ! Berendsen
 taup=0.5          ! Pressure relaxtion time (ps)
 ntf=1,            ! Complete force evaluation
 ntt=3,            ! Langevin thermostat
 gamma_ln=2.0      ! Collision Frequency for thermostat
 ig=-1,            ! Random seed for thermostat
 temp0=298.15      ! Simulation temperature (K)
 ntwx= 1000,       ! Write to trajectory file every ntwx steps
 ntpr= 1000,       ! Print to mdout every ntpr steps
 ntwr= 1000,       ! Write a restart file every ntwr steps
 cut=  8.0,        ! Nonbonded cutoff in Angstroms
 ntr=1,            ! Turn on restraints
 restraintmask=":1-131@CA,C,N", ! atoms to be restrained
 restraint_wt=0.1, ! force constant for restraint
 ntxo=1,           ! Write coordinate file in ASCII format
 ioutfm=0,         ! Write trajectory file in ASCII format
 iwrap=1,          ! iwrap is turned on
/

vim 09.equil.mdin


MD simulations
&cntrl
 imin=0,           ! Perform MD
 nstlim=50000      ! Number of MD steps
 ntx=5,            ! Positions and velocities read formatted
 irest=1,          ! Restart calculation
 ntc=1,            ! No SHAKE on for bonds with hydrogen
 dt=0.001,         ! Timestep (ps)
 ntb=2,            ! Constant Pressure
 ntp=1,            ! Isotropic pressure scaling
 barostat=1        ! Berendsen
 taup=0.5          ! Pressure relaxtion time (ps)
 ntf=1,            ! Complete force evaluation
 ntt=3,            ! Langevin thermostat
 gamma_ln=2.0      ! Collision Frequency for thermostat
 ig=-1,            ! Random seed for thermostat
 temp0=298.15      ! Simulation temperature (K)
 ntwx= 1000,       ! Write to trajectory file every ntwx steps
 ntpr= 1000,       ! Print to mdout every ntpr steps
 ntwr= 1000,       ! Write a restart file every ntwr steps
 cut=  8.0,        ! Nonbonded cutoff in Angstroms
 ntr=1,            ! Turn on restraints
 restraintmask=":1-131@CA,C,N", ! atoms to be restrained
 restraint_wt=0.1, ! force constant for restraint
 ntxo=1,           ! Write coordinate file in ASCII format
 ioutfm=0,         ! Write trajectory file in ASCII format
 iwrap=1,          ! iwrap is turned on
/

Create a submission script that utilizes, above input files to equilibrate the biological system. 

vim mdequilibration.sh

#!/bin/sh                                                                                                                                                                                                                                     
#PBS -N 2nnq_equilibration                                                                                                                                                                                                                    
#PBS -l walltime=04:00:00                                                                                                                                                                                                                     
#PBS -l nodes=2:ppn=28                                                                                                                                                                                                                        
#PBS -j oe                                                                                                                                                                                                                                    
#PBS -q long                                                                                                                                                                                                                                  

cd $PBS_O_WORKDIR

echo "Started Equilibration on `date` "
do_parallel="sander" 

prmtop="../001.tleap_build/2nnq.wet.complex.prmtop"
coords="../001.tleap_build/2nnq.wet.complex" 


MDINPUTS=(01.min 02.equil 03.min 04.min 05.min 06.equil 07.equil 08.equil 09.equil)

for input in ${MDINPUTS[@]}; do

 $do_parallel -O -i ${input}.mdin -o ${input}.mdout -p $prmtop -c ${coords}.rst7 -ref ${coords}.rst7 -x ${input}.trj -inf 
${input}.info -r ${input}.rst7
 coords=$input
done 

echo "Finished Equilibration on `date` "

Submit the job 

qsub md.equilibration.sh

Production

Move into 003.production

Move into 001.restrained

Create 10.prod.mdin 

 MD simulations
&cntrl
 imin=0,           ! Perform MD
 nstlim=5000000,   ! Number of MD steps
 ntx=5,            ! Positions and velocities read formatted
 irest=1,          ! Restart calculation
 ntc=2,            ! SHAKE on for bonds with hydrogen
 dt=0.002,         ! Timestep (ps)
 ntb=2,            ! Constant Pressure
 ntp=1,            ! Isotropic pressure scaling
 barostat=1        ! Berendsen
 taup=0.5          ! Pressure relaxtion time (ps)
 ntf=2,            ! No force evaluation for bonds with hydrogen
 ntt=3,            ! Langevin thermostat
 gamma_ln=2.0      ! Collision Frequency for thermostat
 ig=-1,            ! Random seed for thermostat
 temp0=298.15      ! Simulation temperature (K)
 ntwx= 2500,       ! Write to trajectory file every ntwx steps
 ntpr= 2500,       ! Print to mdout every ntpr steps
 ntwr= 5000000,    ! Write a restart file every ntwr steps
 cut=8.0,          ! Nonbonded cutoff in Angstroms
 ntr=1,            ! Turn on restraints
 restraintmask=":1-287@CA,C,N", ! atoms to be restrained
 restraint_wt=0.1, ! force constant for restraint
 ntxo=1,           ! Write coordinate file in ASCII format
 ioutfm=0,         ! Write trajectory file in ASCII format
 iwrap=1,          ! iwrap is turned on

Create prod.sh 

 #!/bin/sh                                                                                                                                                                                                                                     
#PBS -N 2nnq_production                                                                                                                                                                                                                       
#PBS -l walltime=24:00:00                                                                                                                                                                                                                     
#PBS -l nodes=2:ppn=24                                                                                                                                                                                                                        
#PBS -j oe                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
#PBS -o production.output
#PBS -q long                                                                                                                                                                                                                     

cd $PBS_O_WORKDIR

echo "Started Production on `date` "
#do_parallel="mpirun pmemd.MPI"                                                                                                                                                                                                               
do_cuda="mpirun pmemd.MPI"

prmtop="../../001.tleap_build/2nnq.wet.complex.prmtop"
coords="../../002.equilbration/09.equil"


MDINPUTS=(10.prod)

for input in ${MDINPUTS[@]}; do

 $do_cuda -O -i ${input}.mdin -o ${input}.mdout -p $prmtop -c ${coords}.rst7 -ref ${coords}.rst7 -x ${input}.trj -inf 
${input}.info -r ${input}.rst7
 coords=$input
done

echo "Finished Production on `date` "


Submit the job 

qsub prod.sh

Move into 002.unrestrained

Create 10.prod.mdin 

 MD simulations
&cntrl
 imin=0,           ! Perform MD
 nstlim=5000000    ! Number of MD steps
 ntx=5,            ! Positions and velocities read formatted
 irest=1,          ! Restart calculation
 ntc=2,            ! SHAKE on for bonds with hydrogen
 dt=0.002,         ! Timestep (ps)
 ntb=2,            ! Constant Pressure
 ntp=1,            ! Isotropic pressure scaling
 barostat=1        ! Berendsen
 taup=0.5          ! Pressure relaxtion time (ps)
 ntf=2,            ! No force evaluation for bonds with hydrogen
 ntt=3,            ! Langevin thermostat
 gamma_ln=2.0      ! Collision Frequency for thermostat
 ig=-1,            ! Random seed for thermostat
 temp0=298.15      ! Simulation temperature (K)
 ntwx= 2500,       ! Write to trajectory file every ntwx steps
 ntpr= 2500,       ! Print to mdout every ntpr steps
 ntwr= 5000000,    ! Write a restart file every ntwr steps
 cut=  8.0,        ! Nonbonded cutoff in Angstroms
 ntxo=1,           ! Write coordinate file in ASCII format
 ioutfm=0,         ! Write trajectory file in ASCII format
 iwrap=1,          ! iwrap is turned on
/


Create prod.sh 

 #!/bin/sh                                                                                                                                                                                                                                     
#PBS -N 2nnq_production                                                                                                                                                                                                                       
#PBS -l walltime=24:00:00                                                                                                                                                                                                                     
#PBS -l nodes=2:ppn=24                                                                                                                                                                                                                        
#PBS -j oe                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
#PBS -o production.output
#PBS -q long                                                                                                                                                                                                                     

cd $PBS_O_WORKDIR

echo "Started Production on `date` "
#do_parallel="mpirun pmemd.MPI"                                                                                                                                                                                                               
do_cuda="mpirun pmemd.MPI"

prmtop="../../001.tleap_build/2nnq.wet.complex.prmtop"
coords="../../002.equilbration/09.equil"


MDINPUTS=(10.prod)

for input in ${MDINPUTS[@]}; do

 $do_cuda -O -i ${input}.mdin -o ${input}.mdout -p $prmtop -c ${coords}.rst7 -ref ${coords}.rst7 -x ${input}.trj -inf 
${input}.info -r ${input}.rst7
 coords=$input
done

echo "Finished Production on `date` "


Submit the job 

qsub prod.sh

Analysis

RMSD

How far our ligand moved and how far our receptor moved

Create cpptraj.strip.wat.in 

#!/usr/bin/sh                                                               
parm ../../001.tleap_build/2nnq.wet.complex.prmtop
#read in trajectory                                                         
trajin ../../003.production/001.restrained/10.prod.trj
#read in reference                                                          
reference ../../001.tleap_build/2nnq.wet.complex.rst7
#compute rmsd and align CA to the crystal structure                         
rmsd rms1 reference :1-131@CA
#strip Solvent                                                              
strip :WAT:Na+:Cl-
#create gas-phase trajectory                                                
trajout 2nnq.stripfit.restrained.gas.trj nobox

Run cpptraj 

cpptraj -i cpptraj.strip.wat.in

Create cpptraj.rmsd.lig.in 

#!/usr/bin/sh                                                               
#trajin the trajectory                                                      
trajin 2nnq.stripfit.restrained.gas.trj
#read in the reference                                                      
reference ../../001.tleap_build/2nnq.gas.complex.rst7
#compute the RMSD (do not fit the internal geometries first, included rigid body motions                                                               
#and convert the frames to ns (framenum*.005)                               
rmsd rms1 ":132&!(@H=)" nofit mass out 2nnq.lig.restrained.rmsd.nofit.dat time .005
#histogram the nofit rmsd                                                   
histogram rms1,*,*,.1,* norm out 2nnq.lig.restrained.rmsd.nofit.histogram.dat


Run cpptraj 

cpptraj -p ../../001.tleap_build/2nnq.gas.complex.prmtop -i cpptraj.rmsd.lig.in

Create cpptraj.rmsd.rec.in 

#!/usr/bin/sh                                                                                    
#trajin the trajectory                                                                           
trajin 2nnq.stripfit.restrained.gas.trj
#read in the reference                                                                           
reference ../../001.tleap_build/2nnq.gas.complex.rst7
#compute the RMSD (do not fit the internal geometries first, included rigid body motions         
#and convert the frames to ns (framenum*.005)                                                    
rmsd rms1 ":1-131&!(@H=)" nofit mass out 2nnq.rec.restrained.rmsd.nofit.dat time .005
#histogram the nofit rmsd                                                                        
histogram rms1,*,*,.1,* norm out 2nnq.rec.restrained.rmsd.nofit.histogram.dat

Run cpptraj 

cpptraj -p ../../001.tleap_build/2nnq.gas.complex.prmtop -i cpptraj.rmsd.rec.in

H Bond

Hydrogen bonding

Create cpptraj.hbond.in 

#!/usr/bin/sh                                                                                                                              
#read in trajectory                                                                                                                        
trajin ../../003.production/001.restrained/10.prod.trj
#wrap everything into one periodic cell                                                                                                    
#autoimage                                                                                                                                 
#compute intra and water mediated hydrogen bonds                                                                                           
hbond hb1 :1-288 out 2nnq_sunitinib.hbond.out avgout 2nnq_sunitinib.hbond.avg.dat solventdonor :WAT solventacceptor :WAT@O 
nointramol brid\
geout 2nnq_sunitinib.bridge-water.dat dist 3.0 angle 140

Run cpptraj 

cpptraj -p ../../001.tleap_build/2nnq.wet.complex.prmtop -i cpptraj.hbond.in

MMGBSA

This will analyze how strongly our small molecule binds to our receptor.

Create mmgbsa.in 

mmgbsa 2nnq analysis                                                                                                                    
&general                                                                                                                                   
  interval=1, netcdf=1,                                                                                                                    
  keep_files=0,                                                                                                                            
                                                                                                                                           
/                                                                                                                                          
&gb                                                                                                                                        
  igb=8,                                                                                                                                   
  saltcon=0.0, surften=0.0072,                                                                                                             
  surfoff=0.0, molsurf=0,                                                                                                                  
/                                                                                                                                          
&nmode                                                                                                                                     
  drms=0.001, maxcyc=10000,                                                                                                                
  nminterval=250, nmendframe=2000,                                                                                                         
  nmode_igb=1,                                                                                                                              
/


Create mmgbsa.sh 

#!/bin/bash                                                                                                                                
#PBS -l walltime=35:00:00                                                                                                                  
#PBS -l nodes=1:ppn=24                                                                                                                     
#PBS -N 4qmz_mmgbsa                                                                                                                        
#PBS -V                                                                                                                                    
#PBS -j oe                                                                                                                                 
#PBS -q long-24core                                                                                                                         

cd $PBS_O_WORKDIR 

#Define topology files                                                                                                                     
solv_prmtop="../../001.tleap_build/2nnq.wet.complex.prmtop"
complex_prmtop="../../001.tleap_build/2nnq.gas.complex.prmtop"
receptor_prmtop="../../001.tleap_build/2nnq.gas.receptor.prmtop"
ligand_prmtop="../../001.tleap_build/2nnq.gas.ligand.prmtop"
trajectory="../../003.production/001.restrained/10.prod.trj"
  

#create mmgbsa input file                                                                                                                  
cat >mmgbsa.in<<EOF                                                                                                                        
mmgbsa HIVgp41 analysis                                                                                                                    
&general                                                                                                                                   
  interval=1, netcdf=1,                                                                                                                    
  keep_files=0,                                                                                                                            
                                                                                                                                           
/                                                                                                                                          
&gb                                                                                                                                        
  igb=8,                                                                                                                                   
  saltcon=0.0, surften=0.0072,                                                                                                             
  surfoff=0.0, molsurf=0,                                                                                                                  
/                                                                                                                                          
&nmode                                                                                                                                     
  drms=0.001, maxcyc=10000,                                                                                                                
  nminterval=250, nmendframe=2000,                                                                                                         
  nmode_igb=1,                                                                                                                             
/                                                                                                                                          
EOF                                                                                                                                        
 

 

MMPBSA.py -O -i mmgbsa.in \
           -o  2nnq.mmgbsa.results.dat \
           -eo 2nnq.mmgbsa.per-frame.dat \
           -sp ${solv_prmtop} \
           -cp ${complex_prmtop} \
           -rp ${receptor_prmtop} \
           -lp ${ligand_prmtop} \
            -y ${trajectory}

Submit your script 

qsub mmgbsa.sh

The last line of our 2nnq.mmgbsa.results.dat file shows that our delta G binding is -24.4431 +/- 5.4851.

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