I would suggest using AmberTools 12. It is a free upgrade to the latest
version which has many improvements over the previous version, one of which
should be an improved method for calculating standard deviation.
-Bill
On Tue, May 29, 2012 at 8:53 AM, Cao Yang <muxiachuixue.163.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 29 2012 - 06:00:02 PDT
