Amber TUTORIAL B5: Simulating the Green Fluorescent Protein

Section 1: Preparing the PDB file

pdb4amber -i 1EMA.pdb -o gfp.pdb --dry --reduce

Section 2: Computing partial charges and atom types for CRO

antechamber -fi ccif -i CRO.cif -bk CRO -fo ac -o cro.ac -c bcc -at amber

Section 3: Preparing the residue library and force field parameters for use with LEaP

prepgen -i cro.ac -o cro.prepin -m cro.mc -rn CRO

parmchk2 -i cro.prepin -f prepi -o frcmod.cro -a Y \
         -p $AMBERHOME/dat/leap/parm/parm10.dat

grep -v "ATTN" frcmod.cro > frcmod1.cro # Strip out ATTN lines

parmchk2 -i cro.prepin -f prepi -o frcmod2.cro

Section 4: Creating the topology and coordinate files for simulation

$$$ tleap.in

source leaprc.protein.ff14SB
set default PBRadii mbondi3
loadAmberPrep cro.prepin
loadAmberParams frcmod2.cro
loadAmberParams frcmod1.cro
x = loadPDB gfp.pdb
saveAmberParm x gfp.parm7 gfp.rst7
quit

tleap -f tleap.in

Section 5: Simulations; minimization, heating, equilibration, and production

Minimization

$$$ min.in

  simple generalized Born minimization script
 &cntrl
   imin=1, ntb=0, maxcyc=100, ntpr=10, cut=1000., igb=8, 
 /

sander -O -i min.in -p gfp.parm7 -c gfp.rst7 -o min1.out -r min1.rst7

Heating

$$$ heat.in


Implicit solvent initial heating mdin
 &cntrl
   imin=0, irest=0, ntx=1,
   ntpr=1000, ntwx=1000, nstlim=100000,
   dt=0.002, ntt=3, tempi=10,
   temp0=300, gamma_ln=1.0, ig=-1,
   ntp=0, ntc=2, ntf=2, cut=1000,
   ntb=0, igb=8, ioutfm=1, nmropt=1,
 /
 &wt
   TYPE='TEMP0', ISTEP1=1, ISTEP2=100000,
   VALUE1=10.0, VALUE2=300.0,
 /
 &wt TYPE='END' /

sander -O -i heat.in -p gfp.parm7 -c min1.rst7 -o heat.mdout \
       -x heat.nc -r heat.rst7

Production

$$$ md.in

Implicit solvent molecular dynamics
 &cntrl
   imin=0, irest=1, ntx=5,
   ntpr=1000, ntwx=1000, nstlim=500000,
   dt=0.002, ntt=3, tempi=300,
   temp0=300, gamma_ln=1.0, ig=-1,
   ntp=0, ntc=2, ntf=2, cut=1000,
   ntb=0, igb=8, ioutfm=1,
 /

sander -O -i md.in -p gfp.parm7 -c heat.rst7 -o md1.mdout \
       -x md1.nc -r md1.rst7