I conducted a single trajectory MMGBSA calculation. The results are shown below.
The MD simulations were carried out for 100ns. The complex, a homodimer, was stable. The STD seems to me to be extremely high.
I took note of Jason’s earlier message on MMGBSA statistics (
http://archive.ambermd.org/201202/0317.html) and I’m still perplexed about the very high values of STD.
Any clarification would be most welcome.
Regards
George
Input file:
|--------------------------------------------------------------
|Per-residue GB decomposition
|&general
| interval=4, endframe=10000, verbose=1,
|/
|&gb
| igb=2, saltcon=0.100,
|/
|&decomp
| idecomp=1,
| dec_verbose=1,
|/
|MMPBSA.py Version=13.0
|Solvated complex topology file: 4fqt_solv.prmtop
|Complex topology file: 4fqt.prmtop
|Receptor topology file: 4fqa.prmtop
|Ligand topology file: 4fqb.prmtop
|Initial mdcrd(s): prod_0-100ns.nc
|
|Receptor mask: ":1-126"
|Ligand mask: ":127-252"
|
|Calculations performed using 2500 complex frames.
|
|Generalized Born ESURF calculated using 'LCPO' surface areas
|
|All units are reported in kcal/mole
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -64.8017 6.5714 0.1314
EEL 516.0937 60.8255 1.2165
EGB -480.5187 57.7986 1.1560
ESURF -8.7980 0.7323 0.0146
DELTA G gas 451.2919 60.9252 1.2185
DELTA G solv -489.3166 57.5396 1.1508
DELTA TOTAL -38.0247 6.8780 0.1376
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Received on Thu Feb 12 2015 - 06:30:02 PST
