(unknown charset) Re: [AMBER] MMPBSA final results of MMPBSA.py different fromtutorial

From: (unknown charset) LI An-Bang <anbangli.qq.com>
Date: Sat, 21 May 2016 21:29:04 +0800

Thanks for your reply.
I compared my results with that on the tutorial page.
(http://ambermd.org/tutorials/advanced/tutorial3/py_script/section2.htm )


The GB results are the same, only the nonpolar part of the PB results are different.
The nonpolar parts in my results are shown with components "ENPOLAR" and "EDISPER",
while the nonpolar parts on the webpage are shown only with "ECAVITY".
And the sums of "ENPOLAR" and "EDISPER" are quite different from "ECAVITY".


I pinpoint the difference in my results with "!!" and font color red, as following:


-------------------------------------------------------------------------------
POISSON BOLTZMANN:


Complex:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -2013.3861 20.1108 2.8441
EEL -16938.6434 84.8707 12.0025
EPB -3243.8422 65.3230 9.2381
!!ENPOLAR 1965.5188 6.3800 0.9023
!!EDISPER -1107.5209 6.8746 0.9722


G gas -18952.0295 81.3542 11.5052
!!G solv -2385.8443 64.1413 9.0709


!!TOTAL -21337.8739 41.6822 5.8948




Receptor:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1955.2346 19.0529 2.6945
EEL -16895.0333 84.6812 11.9757
EPB -3269.8301 65.8433 9.3116
!!ENPOLAR 1956.8205 6.3089 0.8922
!!EDISPER -1131.1692 6.4443 0.9114


G gas -18850.2679 80.7202 11.4156
!!G solv -2444.1788 64.7272 9.1538


!!TOTAL -21294.4467 40.4322 5.7180




Ligand:
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -1.8595 2.0320 0.2874
EEL -5.5800 2.0133 0.2847
EPB -30.7641 0.6756 0.0955
!!ENPOLAR 52.1180 0.2043 0.0289
!!EDISPER -50.6514 0.3305 0.0467


G gas -7.4395 3.0299 0.4285
!!G solv -29.2976 0.7438 0.1052


!!TOTAL -36.7370 3.0716 0.4344




Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -56.2921 2.8956 0.4095
EEL -38.0301 3.1822 0.4500
EPB 56.7520 3.5086 0.4962
!!ENPOLAR -43.4196 1.2202 0.1726
!!EDISPER 74.2997 1.3514 0.1911


DELTA G gas -94.3222 3.3476 0.4734
DELTA G solv 87.6321 3.8310 0.5418


!!DELTA TOTAL -6.6901 3.8563 0.5454
-------------------------------------------------------------------------------





------------------ Original ------------------
From: "David A Case";<david.case.rutgers.edu>;
Date: Sat, May 21, 2016 08:25 PM
To: "AMBER Mailing List"<amber.ambermd.org>;

Subject: Re: [AMBER] MMPBSA final results of MMPBSA.py different fromtutorial



On Sat, May 21, 2016, LI An-Bang wrote:
>
> I am going through Amber tutorial A3 "MM-PBSA" to learn how to calculate
> binding energy.
> (Webpage: http://ambermd.org/tutorials/advanced/tutorial3/ )
> And I find the final PBSA results are quite different from that in the
> tutorial.

It would help a lot if you could pinpoint the differences between your outputs
and those in the tutorial. Are your GB results the same as in the tutorial?
Are some components of the PBSA calculation the same and some different?
If so, please do as much analysis as you can do isolate the problem and
describe it concisely.

...thx...dac


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Received on Sat May 21 2016 - 07:00:04 PDT
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