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 >.A<OXT >
total atoms in file:
Leap added missing atoms according to residue templates:
Heavy
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 ()
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 (- 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^
Total mass 162173.797 amu, Density 0.793 g/cc
Added residues.
> charge mol
Total unperturbed charge: 2.000000
Total perturbed charge: 2.000000
> addIons2 mol Cl- 0
Cl- ions required to neutralize.
Adding counter ions to "mol" using 1A grid
Grid extends from solute vdw + 2.51 to 8.51
Resolution: 1.00 Angstrom.
grid build: sec
Calculating grid charges
charges: 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 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
NCYS
WAT
)
(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=, maxcyc=,
ntpr=,
ntr=,
&end
Group input for restrained atoms
100.0
RES
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=, maxcyc=,
ntpr=,
&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
&cntrl
nstlim=, dt=0.002, ntx=, irest=, ntpr=, ntwr=, ntwx=,
tempi =100.0, temp0=300.0, ntt=, tautp=2.0, ig=,
ntb=, ntp=,
ntc=, ntf=,
nrespa=,
&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
&cntrl
nstlim=, dt=0.002, ntx=, irest=, ntpr=, ntwr=, ntwx=,
temp0=300.0, ntt=, tautp=2.0,
ntb=, ntp=,
ntc=, ntf=,
nrespa=,
&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
&cntrl
nstlim=, dt=0.002, ntx=, irest=, ntpr=, ntwr=, ntwx=,
temp0=300.0, ntt=, tautp=2.0,
ntb=, ntp=,
ntc=, ntf=,
nrespa=,
&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 :-
image center familiar
rms first out wt1mg_eq_rms.out :-@CA
trajout wt1mg_eq_nice.crd nobox
$ ptraj wt1mg.parm7 ptraj.in
4. Production
production.in
Constant pressure constant temperature production run
&cntrl
nstlim=, dt=0.002, ntx=, irest=, ntpr=, ntwr=, ntwx=,
temp0=300.0, ntt=, tautp=2.0,
ntb=, ntp=,
ntc=, ntf=,
nrespa=,
&end