利用Amber进行动力学模拟和结合自由能计算

https://www.cgl.ucsf.edu/chimera/download.html

  

   antechamber -i ligand.mol2 -fi mol2 -o ligand.ante.mol2 -fo mol2 

parmchk2 -i ligand.ante.mol2 -f mol2 -o ligand.frcmod
  

tleap

  

   source leaprc.protein.ff14SB
source leaprc.gaff
source leaprc.water.tip3p
  

  

   LIG = loadmol2 ligand.ante.mol2
check LIG
loadamberparams ligand.frcmod
saveoff LIG ligand.lib
saveamberparm LIG ligand.prmtop ligand.inpcrd
  

  

   REC = loadpdb rec.pdb
check REC
saveamberparm REC receptor.prmtopreceptor.inpcrd
  

  

   COM = combine {REC, LIG}
saveamberparm COM com.prmtop com.inpcrd
charge COM
solvatebox COM TIP3PBOX 12.0
saveamberparm COM com_solvated.prmtopcom_solvated.inpcrd
  

  

   Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total943 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

<1> 1
CARG 1
NGLY 1
WAT 13849
)
(norestraints)

Exiting LEaP: Errors = 0; Warnings = 19;Notes = 4.
  

quit

pmemd.cuda -O -i min.in -o min.out -p com_solvated.prmtop -c com_solvated.inpcrd -r min.rst -ref com_solvated.inpcrd

  

   minimise com
&cntrl
imin=1,maxcyc=2000,ncyc=1000,
cut=8.0,ntb=1,
ntc=2,ntf=2,
ntpr=100,
ntr=1, restraintmask=':1-288',
restraint_wt=2.0
/
  

pmemd.cuda -O -i heat.in -o heat.out -p com_solvated.prmtop -c min.rst -r heat.rst -x heat.mdcrd -ref min.rst

  

   heat ras-raf

&cntrl

imin=0,irest=0,ntx=1,

nstlim=25000,dt=0.002,

ntc=2,ntf=2,

cut=8.0, ntb=1,

ntpr=500, ntwx=500,

ntt=3, gamma_ln=2.0,

tempi=0.0, temp0=300.0, ig=-1,

ntr=1, restraintmask=':1-242',

restraint_wt=2.0,

nmropt=1

/

&wt TYPE='TEMP0', istep1=0, istep2=25000,

value1=0.1, value2=300.0, /

&wt TYPE='END' /
  

pmemd.cuda -O -i density.in -o density.out -p com_solvated.prmtop -c heat.rst -r density.rst -x density.mdcrd -ref heat.rst

  

   heat ras-raf
&cntrl
imin=0,irest=1,ntx=5,
nstlim=25000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=1.0,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
temp0=300.0, ig=-1,
ntr=1, restraintmask=':1-242',
restraint_wt=2.0,
/
  

pmemd.cuda -O -i equil.in -o equil.out -p com_solvated.prmtop -c density.rst -r equil.rst -x equil.mdcrd

  

   heat ras-raf
&cntrl
imin=0,irest=1,ntx=5,
nstlim=250000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=300.0, ig=-1,
/
  

process_mdout.pl heat.out density.out equil.out

  

   xmgrace summary.DENSITY
xmgrace summary.TEMP
xmgrace summary.ETOT
  

pmemd.cuda -O -i prod.in -o prod.out -p com_solvated.prmtop -c equil.rst -r prod1.rst -x prod1.mdcrd

  

   heat ras-raf
&cntrl
imin=0,irest=1,ntx=5,
nstlim=500000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=5000, ntwx=5000,
ntt=3, gamma_ln=2.0,
temp0=300.0, ig=-1,
 /
  

python $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o result.dat -sp com_solvated.prmtop -cp com.prmtop -rp receptor.prmtop -lp ligand.prmtop -y prod*.mdcrd

  

   Input 
   file 
   for running PB 
   and GB
   
&general
   
   startframe=
   5, 
   verbose=
   1,
   
# entropy=
   1,
   
/
   
&gb
   
  igb=
   2, saltcon=
   0.100
   
/
   
&pb
   
  istrng=
   0.100,
   
/
  

sbatch -N 1 -p g-v100-1 -c 12 amber.sh

  

   #!/bin/bash

module add Anaconda3/2020.02
source /public/software/.local/easybuild/software/amber/aber20/amber.sh
ulimit -s unlimited
ulimit -l unlimited

antechamber -i ligand.mol2 -fi mol2 -o ligand.ante.mol2 -fo mol2

parmchk2 -i ligand.ante.mol2 -f mol2 -o ligand.frcmod

pdb4amber -i protein.pdb -o rec.pdb --reduce --dry -y --nohyd

tleap -s -f tleap.in

pmemd.cuda -O -i min.in -o min.out -p com_solvated.prmtop -c com_solvated.inpcrd -r min.rst -ref com_solvated.inpcrd

pmemd.cuda -O -i heat.in -o heat.out -p com_solvated.prmtop -c min.rst -r heat.rst -x heat.mdcrd -ref min.rst

pmemd.cuda -O -i density.in -o density.out -p com_solvated.prmtop -c heat.rst -r density.rst -x density.mdcrd -ref heat.rst

pmemd.cuda -O -i equil.in -o equil.out -p com_solvated.prmtop -c density.rst -r equil.rst -x equil.mdcrd

pmemd.cuda -O -i prod.in -o prod1.out -p com_solvated.prmtop -c equil.rst -r prod1.rst -x prod1.mdcrd

python $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o result.dat -sp com_solvated.prmtop -cp com.prmtop -rp receptor.prmtop -lp ligand.prmtop -y prod*.mdcrd