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From: Qin Cai <qcai.uci.edu>

Date: Fri, 31 Aug 2012 13:35:13 -0500

One thing I want to add is that if RES card is used, the output is the total EPB of these residues specified in the card.

Best,

Qin

On Aug 23, 2012, at 12:21 PM, Qin Cai wrote:

*> I think it's because the EPB was calculated per residue in pb when idecomp=3. The output EPB is actually the EPB (or delta EPB in the MMPBSA result) of the last residue. The patch attached to this email should be able to fix this.
*

*>
*

*> Thanks,
*

*> Qin
*

*> <pbsa.patch>
*

*> On Aug 22, 2012, at 12:18 PM, Liu Denis wrote:
*

*>
*

*>> 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
*

*>>
*

*>>
*

*>>
*

*>> --
*

*>> ----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
*

*>>
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

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*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

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Received on Fri Aug 31 2012 - 12:00:03 PDT

Date: Fri, 31 Aug 2012 13:35:13 -0500

One thing I want to add is that if RES card is used, the output is the total EPB of these residues specified in the card.

Best,

Qin

On Aug 23, 2012, at 12:21 PM, Qin Cai wrote:

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Received on Fri Aug 31 2012 - 12:00:03 PDT

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