在上一步的三种体系均进行了对应的结构优化后,根据下面的步骤进行能量的计算。
下面以人类E-selectin-sLex复合物为例进行能量计算,其他两种复合物仅需改变输入文件名(标亮部分)即可。在tleap文件的连接(bond)部分均应按照对应的代表文件进行相应的核对与修改。
在主目录下新建文件夹md_calculate,并将所需的pdb文件拷贝至当前文件夹。
$cd $mkdir md_calculate $cp md_simulations/crystal_human_E-selectin_sLex.pdb md_calculate $cp md_simulations/crystal_human_E-selectin.pdb md_calculate $cp md_simulations/sLex.pdb md_calculate $cd md_calculate
使用vim编辑器在当前文件夹下新建以下三个文件,将其内容粘贴至对应文件中并做相应的修改。
1. complex (tleap_human_complex_MMGBSA.in)
set default PBRadii mbondi2 source leaprc.GLYCAM_06j-1 source oldff/leaprc.ff99SB loadamberparams frcmod.ions234lm_126_tip3p mol = loadpdb ./crystal_human_E-selectin_sLex.pdb #表示不同部分的连接信息,主要有二硫键(蛋白)、糖苷键(配体) # protein # # di-sulfide bond # bond mol.19.SG mol.117.SG bond mol.90.SG mol.109.SG bond mol.158.C2 mol.159.O3 # Neu5Ac - Core-2 Gal bond mol.159.C1 mol.160.O4 # Core-2 Gal - GlcNAc bond mol.162.C1 mol.160.O3 # Fuc - GlcNAc bond mol.160.C1 mol.161.O # GlcNAc - OME charge mol #输出文件,需修改相应的文件名 saveamberparm mol complex_human_E-selectin_sLex_MMGBSA.prmtop complex_human_E-selectin_sLex_MMGBSA.rst7 savepdb mol complex_human_E-selectin_sLex_MMGBSA.pdb quit
2. protein (tleap_human_protein_MMGBSA.in)
set default PBRadii mbondi2 source leaprc.GLYCAM_06j-1 source oldff/leaprc.ff99SB loadamberparams frcmod.ions234lm_126_tip3p mol = loadpdb ./crystal_human_E-selectin.pdb # protein # # di-sulfide bond # bond mol.19.SG mol.117.SG bond mol.90.SG mol.109.SG charge mol saveamberparm mol protein_human_E-selectin_MMGBSA.prmtop protein_human_E-selectin_MMGBSA.rst7 savepdb mol protein_human_E-selectin_MMGBSA.pdb quit
3. ligand (tleap_human_ligand_MMGBSA.in)
set default PBRadii mbondi2 source leaprc.GLYCAM_06j-1 source oldff/leaprc.ff99SB mol = loadpdb ./sLex.pdb # protein # # di-sulfide bond # bond mol.158.C2 mol.159.O3 # Neu5Ac - Core-2 Gal bond mol.159.C1 mol.160.O4 # Core-2 Gal - GlcNAc bond mol.162.C1 mol.160.O3 # Fuc - GlcNAc bond mol.160.C1 mol.161.O # GlcNAc - OME charge mol saveamberparm mol ligand_human_sLex_MMGBSA.prmtop ligand_human_sLex_MMGBSA.rst7 savepdb mol ligand_human_sLex_MMGBSA.pdb quit
在终端输入以下命令来运行tleap
$/path/to/amber/bin/tleap -f tleap_human_complex_MMGBSA.in.in $/path/to/amber/bin/tleap -f tleap_human_protein_MMGBSA.in $/path/to/amber/bin/tleap -f tleap_human_ligand_MMGBSA.in
在md_calculate目录下新建以下文件并进行相应的修改:
_MMPBSA_gb_decomp_com.mdin
File generated by MMPBSA.py &cntrl nsnb=99999, dec_verbose=0, ntb=0, surften=0.0072, extdiel=80.0, ncyc=0, cut=999.0, gbsa=2, imin=5, idecomp=1, igb=2, intdiel = 4, / Residues considered as REC RRES 1 121 END Residues considered as LIG LRES 122 126 END Residues to print RES 1 126 END END
关键词RRES对应的参数为蛋白受体的residue ID范围(eg:1-121); 关键词LRES对应的参数为配体分子的残基范围(eg:122-126); 关键词RES对应的参数为该pdb文件中所有残基范围(ge:1-126)。 所对应的文件均为复合物的pdb.
下面的mdin文件与该文件的修改方法一致
_MMPBSA_gb_decomp_lig.mdin
File generated by MMPBSA.py &cntrl nsnb=99999, dec_verbose=0, ntb=0, surften=0.0072, extdiel=80.0, ncyc=0, cut=999.0, gbsa=2, imin=5, idecomp=1, igb=2, intdiel = 4, / Residues considered as LIG LRES 1 5 END Residues to print RES 1 5 END END
所对应的文件为配体的pdb,所需修改的分子范围均为配体的残基范围
_MMPBSA_gb_decomp_rec.mdin
File generated by MMPBSA.py &cntrl nsnb=99999, dec_verbose=0, ntb=0, surften=0.0072, extdiel=80.0, ncyc=0, cut=999.0, gbsa=2, imin=5, idecomp=1, igb=2, intdiel = 4, / Residues considered as REC RRES 1 121 END Residues to print RES 1 121 END END
所对应的文件为蛋白的pdb,所需修改的分子范围均为蛋白的残基范围。
新建以下文件计算轨迹:
cpptraj_decomp.in
trajin ../md_simulations/produ_complex_human_E-selectin_sLex_WAT.nc 1 100000 100 strip :Na+ trajout human_E-selectin_sLex_MMGBSA.crd go
在终端运行以下命令获得拓扑文件:
/path/to/amber/bin/cpptraj complex_human_E-selectin_sLex.prmtop < cpptraj_decomp.in
在当前文件夹下新建以下文件进行能量计算的提交。
mm_GBSA_DECOMP.in
&general verbose=2, / &gb igb=2, / &decomp idecomp=1, /
新建以下提交文件:
submit.MMGBSA.sh
#!/bin/bash #SBATCH -D /path/to/MMGBSA/calculation/directory #SBATCH -J name #SBATCH --partition=defq #SBATCH --get-user-env #SBATCH --nodes=1 #SBATCH --tasks-per-node=28 source /etc/profile.d/modules.sh srun hostname -s | sort -u >slurm.hosts mpirun -np 28 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mm_GBSA_DECOMP.in -o mm_GBSA_human_E-selectin_sLex_MMGBSA_decomp.out -cp complex_human_E-selectin_sLex_MMGBSA.prmtop -rp protein_human_E-selectin_MMGBSA.prmtop -lp ligand_human_sLex_MMGBSA.prmtop -y human_E-selectin_sLex_MMGBSA.crd -do human_E-selectin_sLex_MMGBSA.dat -use-mdins
在端输入以下命令进行提交
$ bash submit.MMGBSA.sh