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