Hi,
You have not computed the entropy of binding, so what you have is enthalpy component of binding.
Therefore, what you have computed is not true delta G of binding.
Best Regards
Elvis Martis
Mumbai, INDIA.
________________________________________
From: NADIA RAHMAH <nadiiarah.apps.ipb.ac.id>
Sent: 06 July 2017 15:19:42
To: AMBER Mailing List
Subject: Re: [AMBER] MMPBSA Delta total results
Sorry to send not complete results. I didnt tell you this is PB Delta G. PB
Delta total value is positive while GB Delta is negaive, Is it problem or
something error?
|Input file:
|--------------------------------------------------------------
|Sample input file for GB and PB calculation
|&general
|startframe=1, endframe=10000, interval=50,
|verbose=2, keep_files=0,
|/
|&gb
|igb=5, saltcon=0.150,
|/
|&pb
|istrng=0.15, fillratio=4.0
|/
|--------------------------------------------------------------
|MMPBSA.py Version=14.0
|Complex topology file: complexnobox_3wi7rbb.prmtop
|Receptor topology file: protein.prmtop
|Ligand topology file: ligan.prmtop
|Initial mdcrd(s): 3wi7rbb.nc
|
|Receptor mask: ":1-291"
|Ligand mask: ":292"
|Ligand residue name is "UNL"
|
|Calculations performed using 200 complex frames.
|Poisson Boltzmann calculations performed using internal PBSA solver in
mmpbsa_py_energy
|
|Generalized Born ESURF calculated using 'LCPO' surface areas
|
|All units are reported in kcal/mole.
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 912.5936 23.3491
1.6510
ANGLE 2428.7787 34.2154
2.4194
DIHED 3769.6586 21.4600
1.5175
VDWAALS -2466.7203 22.2716
1.5748
EEL -19829.1418 106.3164
7.5177
1-4 VDW 1084.1896 14.5553
1.0292
1-4 EEL 9856.0973 41.1595
2.9104
EGB -2557.6201 85.2699
6.0295
ESURF 89.0527 1.7420
0.1232
G gas -4244.5444 103.4226
7.3131
G solv -2468.5674 84.5367
5.9776
TOTAL -6713.1118 51.4808
3.6402
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 911.3783 23.2978
1.6474
ANGLE 2422.5641 34.0504
2.4077
DIHED 3768.2360 21.4450
1.5164
VDWAALS -2448.4510 22.0682
1.5605
EEL -19821.6598 106.3786
7.5221
1-4 VDW 1083.3272 14.6062
1.0328
1-4 EEL 9857.1039 41.1947
2.9129
EGB -2565.1932 85.3334
6.0340
ESURF 89.9441 1.7262
0.1221
G gas -4227.5013 104.0079
7.3545
G solv -2475.2491 84.5944
5.9817
TOTAL -6702.7503 51.5860
3.6477
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 1.2152 0.9774
0.0691
ANGLE 6.2146 2.0044
0.1417
DIHED 1.4225 0.6671
0.0472
VDWAALS -0.0078 0.3911
0.0277
EEL -0.4298 0.2128
0.0150
1-4 VDW 0.8625 0.4192
0.0296
1-4 EEL -1.0066 0.2333
0.0165
EGB -2.4506 0.0873
0.0062
ESURF 1.6260 0.0096
0.0007
G gas 8.2706 2.4641
0.1742
G solv -0.8245 0.0865
0.0061
TOTAL 7.4461 2.4730
0.1749
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND -0.0000 0.0001
0.0000
ANGLE 0.0000 0.0001
0.0000
DIHED 0.0000 0.0000
0.0000
VDWAALS -18.2614 1.2729
0.0900
EEL -7.0523 1.8874
0.1335
1-4 VDW -0.0000 0.0001
0.0000
1-4 EEL -0.0000 0.0000
0.0000
EGB 10.0237 1.5415
0.1090
ESURF -2.5175 0.0801
0.0057
DELTA G gas -25.3137 2.2277
0.1575
DELTA G solv 7.5062 1.5431
0.1091
DELTA TOTAL -17.8075 1.8112
0.1281
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
POISSON BOLTZMANN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 912.5936 23.3491
1.6510
ANGLE 2428.7787 34.2154
2.4194
DIHED 3769.6586 21.4600
1.5175
VDWAALS -2466.7203 22.2716
1.5748
EEL -19829.1418 106.3164
7.5177
1-4 VDW 1084.1896 14.5553
1.0292
1-4 EEL 9856.0973 41.1595
2.9104
EPB -2639.8863 86.9608
6.1491
ENPOLAR 2191.4591 8.4002
0.5940
EDISPER -1130.7876 9.7908
0.6923
G gas -4244.5444 103.4226
7.3131
G solv -1579.2148 86.0073
6.0816
TOTAL -5823.7592 56.4697
3.9930
Receptor:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 911.3783 23.2978
1.6474
ANGLE 2422.5641 34.0504
2.4077
DIHED 3768.2360 21.4450
1.5164
VDWAALS -2448.4510 22.0682
1.5605
EEL -19821.6598 106.3786
7.5221
1-4 VDW 1083.3272 14.6062
1.0328
1-4 EEL 9857.1039 41.1947
2.9129
EPB -2660.8632 86.9206
6.1462
ENPOLAR 2190.4601 8.3759
0.5923
EDISPER -1139.5953 9.7842
0.6919
G gas -4227.5013 104.0079
7.3545
G solv -1609.9985 85.9000
6.0740
TOTAL -5837.4998 55.4874
3.9235
Ligand:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 1.2152 0.9774
0.0691
ANGLE 6.2146 2.0044
0.1417
DIHED 1.4225 0.6671
0.0472
VDWAALS -0.0078 0.3911
0.0277
EEL -0.4298 0.2128
0.0150
1-4 VDW 0.8625 0.4192
0.0296
1-4 EEL -1.0066 0.2333
0.0165
EPB -2.2980 0.0776
0.0055
ENPOLAR 14.9804 0.1359
0.0096
EDISPER -13.3213 0.0859
0.0061
G gas 8.2706 2.4641
0.1742
G solv -0.6389 0.1582
0.0112
TOTAL 7.6317 2.4782
0.1752
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND -0.0000 0.0001
0.0000
ANGLE 0.0000 0.0001
0.0000
DIHED 0.0000 0.0000
0.0000
VDWAALS -18.2614 1.2729
0.0900
EEL -7.0523 1.8874
0.1335
1-4 VDW -0.0000 0.0001
0.0000
1-4 EEL -0.0000 0.0000
0.0000
EPB 23.2749 5.0209
0.3550
ENPOLAR -13.9814 0.2315
0.0164
EDISPER 22.1291 0.5543
0.0392
DELTA G gas -25.3137 2.2277
0.1575
DELTA G solv 31.4226 5.0797
0.3592
DELTA TOTAL 6.1089 4.1135
0.2909
On Thu, Jul 6, 2017 at 4:27 PM, Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> HI,
> I assume this delta G is the results of either PB or GB calculations.
> In the absence of entropy calculations, this delta G total reflects only
> the enthalpy component and hence not the true delta G binding.
>
> Best Regards
> Elvis Martis
> Mumbai, INDIA.
>
> ________________________________________
> From: NADIA RAHMAH <nadiiarah.apps.ipb.ac.id>
> Sent: 06 July 2017 12:45:40
> To: AMBER Mailing List
> Subject: [AMBER] MMPBSA Delta total results
>
> Hello Amber Users, I want to ask about MMPBSA results, at the end of the
> results, I get DELTA TOTAL :
>
> DELTA G gas -24.9391 2.2411
> 0.1585
> DELTA G solv 34.0352 3.5423
> 0.2505
>
> DELTA TOTAL 9.0961 3.7742
> 0.2669
>
> I want to ask, is DELTA TOTAL same with Delta G Binding? because I dont
> find Delta G Binding in my results. and the delta total value is so
> positive. Thanks
> --
>
> *Regards,*
> *Nadia Rahmah*
> *Department of Physics Undergraduate Student - 2013Bogor Agricultural
> University*
> _______________________________________________
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>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*Regards,*
*Nadia Rahmah*
*Department of Physics Undergraduate Student - 2013Bogor Agricultural
University*
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Received on Thu Jul 06 2017 - 03:30:02 PDT
