MMPBSA/MMGBSA应用于对接模型的筛选

kunkun

原文:Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking†

文献结果表明隐式模型下的MMGBSA的模拟效果最好..甚至比显式模型更好...
FF02力场的参数也比AMBER14SB更好...（我在考虑要不要用最新的fb15或则ff15ipq)
表示很疑问？？有大神帮忙分析下么！！我到底要不要参考它.....

我用隐式模型计算速度比显式模型还要慢....我的天。愁死个ren

另外还有个疑问。隐式模型下MMPBSA.py的运行该怎么生成solvent的拓扑文件啊...  其中-sp项和-cp项我按照一个文件输入了..

tleap:生成..
        # make tleap
        tleap = '''source leaprc.protein.ff15ipq
com = loadpdb %s
a = loadpdb antigen.pdb
ab = loadpdb antibody.pdb
set default PBRadii mbondi2
saveamberparm com complex.prmtop complex.inpcrd
saveamberparm a antigen.prmtop antigen.inpcrd
saveamberparm ab antibody.prmtop antibody.inpcrd
saveamberparm com complex_sol.prmtop complex_sol.inpcrd
savepdb com complex_sol.pdb
quit

''' % (self.pdbfile)

mmpbsa运行:
def run_mmgbsa(self):
    print 'Running MMGBSA...'
    os.system('mpirun --allow-run-as-root -np 44 MMPBSA.py.MPI -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat \
    -sp complex_sol.prmtop \
    -cp complex.prmtop \
    -rp antigen.prmtop \
    -lp antibody.prmtop \
    -y md.mdcrd > mmpbsa.log 2>&1')

lijiayisjtu

侯老师组 发过一篇Chemical reviews 里面有提到