Amber learning note A8: Loop Dynamics of the HIV-1 Integrase Core Domain

 1. Prepare Input File

$ tleap

>source leaprc.protein.ff14SB

----- Source: /home/wangq/Programs/amber16/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /home/wangq/Programs/amber16/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log
Loading parameters: /home/wangq/Programs/amber16/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /home/wangq/Programs/amber16/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /home/wangq/Programs/amber16/dat/leap/lib/amino12.lib
Loading library: /home/wangq/Programs/amber16/dat/leap/lib/aminoct12.lib
Loading library: /home/wangq/Programs/amber16/dat/leap/lib/aminont12.lib

> loadoff mg.off

Loading library: ./mg.off

> mol = loadpdb wt1mg.pdb

Loading PDB file: ./wt1mg.pdb
  Added missing heavy atom: .R<CGLN 154>.A<OXT 18>
  total atoms in file: 1189
  Leap added 1192 missing atoms according to residue templates:
       1 Heavy
       1191 H / lone pairs

> source leaprc.water.tip3p

----- Source: /home/wangq/Programs/amber16/dat/leap/cmd/leaprc.water.tip3p
----- Source of /home/wangq/Programs/amber16/dat/leap/cmd/leaprc.water.tip3p done
Loading library: /home/wangq/Programs/amber16/dat/leap/lib/atomic_ions.lib
Loading library: /home/wangq/Programs/amber16/dat/leap/lib/solvents.lib
Loading parameters: /home/wangq/Programs/amber16/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
Loading parameters: /home/wangq/Programs/amber16/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)

> solvateBox mol TIP3P 10 

  Solute vdw bounding box:              49.995 53.684 37.063
  Total bounding box for atom centers:  69.995 73.684 57.063
  Solvent unit box:                     18.774 18.774 18.774
  Total vdw box size:                   73.439 76.851 60.149 angstroms.
  Volume: 339472.593 A^3 
  Total mass 162173.797 amu,  Density 0.793 g/cc
  Added 8064 residues.

> charge mol

Total unperturbed charge:   2.000000
Total perturbed charge:     2.000000

> addIons2 mol Cl- 0

2 Cl- ions required to neutralize.
Adding 2 counter ions to "mol" using 1A grid
Grid extends from solute vdw + 2.51  to  8.51
Resolution:      1.00 Angstrom.
grid build: 1 sec
Calculating grid charges
charges: 149 sec
Placed Cl- in mol at (0.54, -17.17, 29.94).
Placed Cl- in mol at (34.54, -37.17, -19.06).

Done adding ions.

　　addions: simply draw a grid around the solute and places ions at grid points where the energies are lowest.  This approach will ignore water molecules in locating where to place the ion and if the chosen location overlaps a water molecule, the water is deleted and replaced with the ion.

　　addions2: it treats solvent molecules the same as solute.

 > saveAmberParm mol wt1mg.parm7 wt1mg.crd

Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 468 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 - 
   these don't have chain types marked:

    res    total affected

    CGLN    1
    NCYS    1
    WAT    8064
  )
 (no restraints)

2. Energy Minimization

$ ambpdb -p wt1mg.parm7 -c wt1mg.crd > wt1mg_solvated.pdb

min.in

Minimization with Cartesian restraints for the solute 
 &cntrl 
 imin=1, maxcyc=200, 
 ntpr=5, 
 ntr=1, 
 &end 
Group input for restrained atoms 
100.0 
RES 1 155
END
END

$ cp wt1mg.crd wt1mg.rst

$ sander -O -i min.in -p wt1mg.parm7 -c wt1mg.crd -r wt1mg_min.rst -o wt1mg_min_water.out -ref wt1mg.rst

min_all.in

Minimization of the entire molecular system
 &cntrl
  imin=1, maxcyc=200, 
  ntpr=5,
 &end

$ sander -O -i min_all.in -p wt1mg.parm7 -c wt1mg_min_water.rst -r wt1mg_min_all.rst -o wt1mg_min_all.out

3. Equilibration

eq_v.in

Heating up the system equilibration stage 1
 &cntrl
  nstlim=5000, dt=0.002, ntx=1, irest=0, ntpr=500, ntwr=5000, ntwx=5000,
  tempi =100.0, temp0=300.0, ntt=1, tautp=2.0, ig=209858,
  ntb=1, ntp=0,
  ntc=2, ntf=2,
  nrespa=2,
&end

$ sander -O -i eq_v.in -p wt1mg.parm7 -c wt1mg_min_all.rst -r wt1mg_eq_v.rst -x wt1mg_eq_v.crd -o wt1mg_eq_v.out

$ grep TEMP wt1mg_eq_v.out | awk '{print $6, $9}' > temp.dat

eq_pt.in

Constant pressure constant temperature equilibration stage 2
 &cntrl
  nstlim=5000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=5000, ntwx=5000,
  temp0=300.0, ntt=1, tautp=2.0,
  ntb=2, ntp=1,
  ntc=2, ntf=2,
  nrespa=1,
&end

$ sander -O -i eq_pt.in -p wt1mg.parm7 -c wt1mg_eq_v.rst -r wt1mg_eq_pt.rst -x wt1mg_eq_pt.crd -o wt1mg_eq_pt.out

eq_pt1.in

Constant pressure constant temperature equilibration stage 3
 &cntrl
  nstlim=50000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=5000, ntwx=5000,
  temp0=300.0, ntt=1, tautp=2.0,
  ntb=2, ntp=1,
  ntc=2, ntf=2,
  nrespa=1,
&end

$ sander -O -i eq_pt1.in -p wt1mg.parm7 -c wt1mg_eq_v.rst -r wt1mg_eq_pt1.rst -x wt1mg_eq_pt1.crd -o wt1mg_eq_pt1.out

ptraj.in

trajin wt1mg_eq.crd
center :1-154
image center familiar
rms first out wt1mg_eq_rms.out :3-152@CA
trajout wt1mg_eq_nice.crd nobox

$ ptraj wt1mg.parm7 ptraj.in

4. Production

production.in

Constant pressure constant temperature production run
 &cntrl
  nstlim=500000, dt=0.002, ntx=5, irest=1, ntpr=500, ntwr=5000, ntwx=5000,
  temp0=300.0, ntt=1, tautp=2.0,
  ntb=2, ntp=1,
  ntc=2, ntf=2,
  nrespa=1,
&end

5. Analysis