Hi everybody,
I came across a problem in entropy and decomping calculation with MMPBSA. The standard deviation is abnormally high in both case.
1. High standard deviation in entropy calculation
The entropy of 20 frames were calculated by NMode with the following input file:
Input file for running entropy calculations using NMode
&general
startframe=201, keep_files=2,
strip_mask=":WAT:Cl-:CIO:Cs+:IB:K+:Li+:Na+:Rb+"
/
&nmode
nmstartframe=1,
nminterval=10, nmode_igb=1, nmode_istrng=0.1,
/
The result is as following:
Complex:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: 16.7223 0.0000
Rotational: 17.0094 0.0028
Vibrational: 2452.2343 4.1753
Total: 2485.9660 4.1757
Receptor:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: 16.7119 0.0000
Rotational: 16.9984 0.0026
Vibrational: 2432.7994 3.1862
Total: 2466.5098 3.1868
Ligand:
Entropy Term Average Std. Dev.
-----------------------------------------------------------
Translational: 12.7647 0.0000
Rotational: 10.2737 0.0000
Vibrational: 15.7722 0.0002
Total: 38.8106 0.0002
DELTA S total= -19.3544 +/- 86.2259
-------------------------------------------------------------------------------
I use AmberTools 1.5 with all bugfix. The total standard deviation is extremely high. Maybe AmberTools 12 could get over this? Any suggestions?
2. High standard deviation in decomping calculation
Input:
Per-residue PB decomposition
&general
startframe=201, endframe=500, verbose=1,
/
&pb
istrng=0.100, cavity_surften=0.03252, cavity_offset=0.92,
/
&decomp
idecomp=1,
dec_verbose=1,
/
Output:
Total Energy Decomposition:
Residue | Location | Internal | van der Waals | Electrostatic | Polar Solvation | Non-Polar Solv. | TOTAL
VAL 1 | R VAL 1 | 0.000 +/- 4.630 | -0.000 +/- 1.350 | -0.095 +/- 20.783 | 0.095 +/- 19.466 | 0.000 +/- 0.181 | -0.000 +/- 28.882
ASP 379 | R ASP 379 | 0.000 +/- 2.416 | 1.127 +/- 1.622 | -12.206 +/- 11.846 | 6.517 +/- 8.712 | -0.082 +/- 0.020 | -4.644 +/- 14.990
I use AmberTools 1.5 with all bugfix. The total standard deviation is extremely high. Any suggestions?
Many thanks!
Cao Yang,
Zhejiang University
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Received on Tue May 29 2012 - 06:00:02 PDT
