I make some supplement
There will be same result in GBSA with idecomp = 1 and 3
but different in PBSA
I use Amber12 and AmberTool12, all bug-fixes were applied.
Here are input files for MMPBSA.py
|Input file:
|--------------------------------------------------------------
|&general
| startframe = 5501, endframe = 6000, interval = 5,
| verbose = 2, keep_files = 0,
|/
|&pb
| ,
|/
|&decomp
| idecomp = 1, dec_verbose = 2,
|/
|Input file:
|--------------------------------------------------------------
|&general
| startframe = 5501, endframe = 6000, interval = 5,
| verbose = 2, keep_files = 0,
|/
|&pb
| ,
|/
|&decomp
| idecomp = 3, dec_verbose = 2,
|/
Results were in my previous mail
2012/8/22 Ray Luo <rayhuangluo.gmail.com>:
> Qin,
>
> Do you understand this?
>
> Ray Luo, Ph.D.
>
> Begin forwarded message:
>
> From: Liu Denis <cndenis.gmail.com>
> Date: August 22, 2012 5:03:56 AM EDT
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] Diffenent EPB in MMPBSA result with
> Reply-To: AMBER Mailing List <amber.ambermd.org>
>
> Dear AMBER Members:
> I calculated MMPBSA with idecomp = 1 and 3, the EPB output is
> very different.
> EPB with idecomp=1 is same as idecomp=0.
> Is it normal and why?
>
> Here is result with idecomp = 3:
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> BOND 0.0000 0.0001
> 0.0000
> ANGLE -0.0000 0.0000
> 0.0000
> DIHED -0.0000 0.0000
> 0.0000
> VDWAALS -38.2142 2.4703
> 0.3459
> EEL -10.4690 6.9120
> 0.9679
> 1-4 VDW -0.0000 0.0001
> 0.0000
> 1-4 EEL 0.0000 0.0000
> 0.0000
> EPB 15.3685 2.3473
> 0.3287
> ENPOLAR -23.5715 1.2483
> 0.1748
> EDISPER 41.0299 1.2261
> 0.1717
>
> DELTA G gas -48.6832 6.6882
> 0.9365
> DELTA G solv 32.8270 2.4099
> 0.3375
>
> DELTA TOTAL -15.8562 7.5172
> 1.0526
>
>
>
> Here is idecomp = 1
>
> Differences (Complex - Receptor - Ligand):
> Energy Component Average Std. Dev. Std. Err. of
> Mean
> -------------------------------------------------------------------------------
> BOND 0.0000 0.0001
> 0.0000
> ANGLE -0.0000 0.0000
> 0.0000
> DIHED -0.0000 0.0000
> 0.0000
> VDWAALS -38.2142 2.4703
> 0.3459
> EEL -10.4690 6.9120
> 0.9679
> 1-4 VDW -0.0000 0.0001
> 0.0000
> 1-4 EEL 0.0000 0.0000
> 0.0000
> EPB 32.5072 4.8192
> 0.6748
> ENPOLAR -23.5715 1.2483
> 0.1748
> EDISPER 41.0299 1.2261
> 0.1717
>
> DELTA G gas -48.6832 6.6882
> 0.9365
> DELTA G solv 49.9657 4.8976
> 0.6858
>
> DELTA TOTAL 1.2825 5.2511
> 0.7353
> --
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>
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Received on Wed Aug 22 2012 - 10:30:04 PDT
