环肽-靶标蛋白的Amber分子动力学模拟

准备好对接后的蛋白pro.pdb和配体环肽文件test.mo

第一步：

python 00_make_single_lig.py test.mol2 test_LIG_raw.mol2

00_make_single_lig.py文件如下：

#!/usr/bin/env python3
import sys

if len(sys.argv) != 3:
    print("Usage: python 00_make_single_lig.py input.mol2 output.mol2")
    sys.exit(1)

infile = sys.argv[1]
outfile = sys.argv[2]

section = None

with open(infile, "r") as fin, open(outfile, "w") as fout:
    for line in fin:
        if line.startswith("@<TRIPOS>"):
            section = line.strip()
            fout.write(line)

            if section == "@<TRIPOS>SUBSTRUCTURE":
                fout.write("     1 LIG         1 GROUP             0 ****  ****    0 ROOT\n")
            continue

        if section == "@<TRIPOS>ATOM":
            parts = line.split()
            if len(parts) >= 9:
                atom_id = int(parts[0])
                atom_name = parts[1]
                x = float(parts[2])
                y = float(parts[3])
                z = float(parts[4])
                atom_type = parts[5]
                charge = float(parts[8])

                fout.write(
                    f"{atom_id:7d} {atom_name:<8s} "
                    f"{x:10.4f} {y:10.4f} {z:10.4f} "
                    f"{atom_type:<8s} {1:5d} {'LIG':<8s} {charge:10.6f}\n"
                )
            else:
                fout.write(line)

        elif section == "@<TRIPOS>SUBSTRUCTURE":
            continue

        else:
            fout.write(line)

第二步：antechamber，由于环肽原子量很多，这一步要持续几个小时，移植到能量收敛到0.0005.

antechamber -i test_LIG_raw.mol2 -fi mol2 \
            -o LIG.mol2 -fo mol2 \
            -at gaff2 -c bcc -nc 0 \
            -rn LIG -s 2

第三步：

parmchk2 -i LIG.mol2 -f mol2 -o LIG.frcmod -s gaff2

第四步：处理蛋白

pdb4amber -i pro.pdb -o pro_amber.pdb --reduce --dry

第五步：继续处理单边加氢等：

awk '
/^ATOM/ || /^HETATM/ {
    atom=substr($0,13,4)
    gsub(/ /,"",atom)
    if (atom ~ /^H/) next
}
{print}
' pro_amber.pdb > pro_amber_noH.pdb

第六步：

将配体受体合并：

tleap -f 01_tleap_complex.in | tee 01_tleap_complex.log

01_tleap_complex.in文件如下：

source leaprc.protein.ff19SB
source leaprc.gaff2
source leaprc.water.opc

loadamberparams LIG.frcmod

pro = loadpdb pro_amber_noH.pdb
lig = loadmol2 LIG.mol2

complex = combine {pro lig}

check complex
charge complex

solvateoct complex OPCBOX 10.0

addionsrand complex Na+ 0
addionsrand complex Cl- 0

saveamberparm complex complex.prmtop complex.inpcrd
savepdb complex complex_solvated.pdb

quit

第八步：就是正常MD流程：

1. 限制性最小化：02_min1.in

   Minimization 1: solvent and ions, solute restrained
   &cntrl
   imin=1,
   maxcyc=10000,
   ncyc=5000,
   cut=10.0,
   ntb=1,

   ntr=1,
   restraint_wt=10.0,
   restraintmask='!:WAT,Na+,Cl-',
   /
   END

2. 全体系最小化 03_min2.in

   Minimization 2: whole system
   &cntrl
   imin=1,
   maxcyc=10000,
   ncyc=5000,
   cut=10.0,
   ntb=1,
   /
   END

3. 升温04_heat.in

   Heating from 0 to 300 K
   &cntrl
   imin=0,
   irest=0,
   ntx=1,

   ntb=1,
   cut=10.0,

   nstlim=250000,
   dt=0.002,

   tempi=0.0,
   temp0=300.0,

   ntc=2,
   ntf=2,

   ntt=3,
   gamma_ln=2.0,

   ntpr=1000,
   ntwx=5000,
   ntwr=5000,

   ntr=1,
   restraint_wt=5.0,
   restraintmask='!:WAT,Na+,Cl-',

   nmropt=1,
   /
   &wt TYPE='TEMP0', istep1=0, istep2=250000, value1=0.0, value2=300.0 /
   &wt TYPE='END' /
   END

4. NPT 平衡，有弱限制 05_eq1.in

   NPT equilibration with weak restraint
   &cntrl
   imin=0,
   irest=1,
   ntx=5,

   ntb=2,
   ntp=1,
   taup=2.0,
   cut=10.0,

   nstlim=500000,
   dt=0.002,

   temp0=300.0,
   ntc=2,
   ntf=2,

   ntt=3,
   gamma_ln=2.0,

   ntpr=1000,
   ntwx=5000,
   ntwr=5000,

   ntr=1,
   restraint_wt=1.0,
   restraintmask='!:WAT,Na+,Cl-',
   /
   END

5. NPT 平衡，无限制 06_eq2.in

   NPT equilibration without restraint
   &cntrl
   imin=0,
   irest=1,
   ntx=5,

   ntb=2,
   ntp=1,
   taup=2.0,
   cut=10.0,

   nstlim=500000,
   dt=0.002,

   temp0=300.0,
   ntc=2,
   ntf=2,

   ntt=3,
   gamma_ln=2.0,

   ntpr=1000,
   ntwx=5000,
   ntwr=5000,
   /
   END

6. 生产模拟，单段 10 ns 07_prod.in

   Production MD
   &cntrl
   imin=0,
   irest=1,
   ntx=5,

   ntb=2,
   ntp=1,
   taup=2.0,
   cut=10.0,

   nstlim=5000000,
   dt=0.002,

   temp0=300.0,
   ntc=2,
   ntf=2,

   ntt=3,
   gamma_ln=2.0,

   ntpr=5000,
   ntwx=5000,
   ntwr=50000,

   ioutfm=1,
   ntxo=2,
   /
   END

9.执行运行命令run_md.sh

#!/bin/bash
set -e

PMEMD=pmemd.cuda

echo "Step 1: restrained minimization"
$PMEMD -O \
  -i 02_min1.in \
  -o 02_min1.out \
  -p complex.prmtop \
  -c complex.inpcrd \
  -r 02_min1.rst7 \
  -ref complex.inpcrd

echo "Step 2: full minimization"
$PMEMD -O \
  -i 03_min2.in \
  -o 03_min2.out \
  -p complex.prmtop \
  -c 02_min1.rst7 \
  -r 03_min2.rst7

echo "Step 3: heating"
$PMEMD -O \
  -i 04_heat.in \
  -o 04_heat.out \
  -p complex.prmtop \
  -c 03_min2.rst7 \
  -r 04_heat.rst7 \
  -x 04_heat.nc \
  -ref 03_min2.rst7

echo "Step 4: NPT equilibration with restraint"
$PMEMD -O \
  -i 05_eq1.in \
  -o 05_eq1.out \
  -p complex.prmtop \
  -c 04_heat.rst7 \
  -r 05_eq1.rst7 \
  -x 05_eq1.nc \
  -ref 04_heat.rst7

echo "Step 5: NPT equilibration without restraint"
$PMEMD -O \
  -i 06_eq2.in \
  -o 06_eq2.out \
  -p complex.prmtop \
  -c 05_eq1.rst7 \
  -r 06_eq2.rst7 \
  -x 06_eq2.nc

echo "Step 6: production MD"

prev=06_eq2.rst7

for i in $(seq -w 1 10)
do
  echo "Production segment ${i}"

  $PMEMD -O \
    -i 07_prod.in \
    -o prod_${i}.out \
    -p complex.prmtop \
    -c ${prev} \
    -r prod_${i}.rst7 \
    -x prod_${i}.nc \
    -inf prod_${i}.info

  prev=prod_${i}.rst7
done

echo "MD finished."

最后运行：

chmod +x run_md.sh
./run_md.sh