运用AMBER，MMPBSA计算binding free energy，结果出错，complex的VDWAALS异常的大； |Input file:
|--------------------------------------------------------------
|Per-residue GB and PB decomposition
|&general
| startframe=1,
| endframe=2,
| interval=1,
| verbose=1,
|/
|&pb
|istrng=0.100,
|/
|&decomp
|idecomp=1, print_res="20-27; 137-140; 50-52; 317-319",
|dec_verbose=1,
|/
|--------------------------------------------------------------
|Complex topology file:   com-mmpbsa.prmtop
|Receptor topology file:    pro-mmpbsa.prmtop
|Ligand topology file:    lig.prmtop
|Initial mdcrd(s):      prod1.mdcrd
|
|Best guess for receptor mask: ":1-396"
|Best guess forligandmask: ":397"
|Ligand residue name is "MOL"
|
|Calculations performed using 2 frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in sander.
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component    Average    Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS     65535622.9707      0.0000    0.0000
EEL       -28855.4098      0.0000    0.0000
EPB        -3551.0980      0.0000    0.0000
ECAVITY       84.1394      0.0000    0.0000
G gas     65506767.5609      0.0000    0.0000
G solv       -3466.9586      0.0000    0.0000
TOTAL     65503300.6023      0.0000    0.0000
Receptor:
Energy Component    Average    Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS      -3156.9009      0.0000    0.0000
EEL       -28678.5729      0.0000    0.0000
EPB        -3585.6259      0.0000    0.0000
ECAVITY       84.4270      0.0000    0.0000
G gas       -31835.4738      0.0000    0.0000
G solv       -3501.1989      0.0000    0.0000
TOTAL       -35336.6727      0.0000    0.0000
Ligand:
Energy Component    Average    Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS        1.9849      0.0000    0.0000
EEL        -30.5018      0.0000    0.0000
EPB       -140.0822      0.0000    0.0000
ECAVITY        1.6376      0.0000    0.0000
G gas        -28.5169      0.0000    0.0000
G solv      -138.4446      0.0000    0.0000
TOTAL       -166.9615      0.0000    0.0000
Differences (Complex - Receptor - Ligand):
Energy Component    Average    Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS     65538777.8867      0.0000    0.0000
EEL       -146.3351      0.0000    0.0000
EPB        174.6101      0.0000    0.0000
ECAVITY       -1.9252      0.0000    0.0000
DELTA G gas   65538631.5516      0.0000    0.0000
DELTA G solv     172.6849      0.0000    0.0000
DELTA G binding = 65538804.2366 /-  0.0000     0.0000
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
WARNINGS:
igb=5 should be used with either mbondi2 or bondi pbradii set. Yours are modified Bondi radii (mbondi)
请高手分析啊

顶顶啊     

高手帮忙啊？

自己成功解决了，是因为top文件不匹配的原因，解决方案是：
将跑MD的com-wat.pdb复制，另命名为pro-mmpbsa.pdb和com-mmpbsa.pdb，手动删除里面的水分子，或者底物，然后用tleap-mmpbsa.in生成MMPBSA的pro-mmpbsa.inpcrd和pro-mmpbsa.prmtop,com-mmpbsa.inpcrd和com-mmpbsa.prmtop,再跑MMPBSA就可以了