El 22/08/12 19:18, Liu Denis escribió:
> 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
>> --
>> ----GnuPG Public Key----
>> Key ID: 0x488C9571
>> Fingerprint: C292 D888 D713 4D13 57F0 C07D 16F3 10C9 488C 9571
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
Hi Liu,
I think that something like what you have observed was discussed
recently in the list. Look here:
http://archive.ambermd.org/201205/0195.html
Cheers,
--
Miguel
Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombardia.afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 22 2012 - 10:30:05 PDT
