Ren,
If you look at the individual free energies, G_complex, G_prot, and
G_lig, the differences are less than 2%. However, delta G = G_complex
- G_prot - G_lig amplifies the percent difference because the values
are much much smaller.
So the difference you see is not unreasonable.
All the best,
Ray
On Wed, Aug 1, 2012 at 1:45 PM, Kong, Ren <rkong.tmhs.org> wrote:
> Hi Ray,
>
>
>
> Thank you so much for the reply. It seems the STD for every item is not so big...
>
>
> Differences (Complex - Receptor - Ligand):
>
> Differences (Complex - Receptor - Ligand):
>
> Energy Component Average Std. Dev. Std. Err. of Mean
>
> Energy Component Average Std. Dev. Std. Err. of Mean
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> VDWAALS -51.6704 4.4471 0.3145
>
> VDWAALS -51.6704 4.4471 0.3145
>
> EEL 136.5886 12.1097 0.8563
>
> EEL 136.5886 12.1097 0.8563
>
> EGB -85.2148 11.2510 0.7956
>
> EPB -111.3002 10.5839 0.7484
>
> ESURF -3.8562 0.3254 0.0230
>
> ECAVITY -4.6794 0.3995 0.0282
>
>
> DELTA G gas 84.9182 11.8663 0.8391
>
> DELTA G gas 84.9182 11.8663 0.8391
>
> DELTA G solv -89.0710 11.2012 0.7920
>
> DELTA G solv -115.9796 10.5205 0.7439
>
>
>
> DELTA G binding = -4.1529 +/- 3.2338 0.2287
>
>
>
>
>
> DELTA G binding = -31.0614 +/- 5.3846 0.3807
>
>
>
>
>
> GENERALIZED BORN:
>
> POISSON BOLTZMANN:
>
>
> Complex:
>
> Complex:
>
> Energy Component Average Std. Dev. Std. Err. of Mean
>
> Energy Component Average Std. Dev. Std. Err. of Mean
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> VDWAALS -4588.9601 34.8088 2.4614
>
> VDWAALS -4588.9601 34.8088 2.4614
>
> EEL -46396.8356 107.4889 7.6006
>
> EEL -46396.8356 107.4889 7.6006
>
> EGB -7028.7312 77.1243 5.4535
>
>
>
>
>
> EPB -7128.3657 73.6705 5.2093
>
> ESURF 184.7275 1.4006 0.0990
>
>
>
>
>
> ECAVITY 199.5712 1.0756 0.0761
>
>
> G gas -50985.7957 109.2466 7.7249
>
> G gas -50985.7957 109.2466 7.7249
>
> G solv -6844.0037 76.5618 5.4137
>
>
>
>
>
> G solv -6928.7945 73.2458 5.1793
>
>
> TOTAL -57829.7994 64.1770 4.5380
>
> TOTAL -57914.5902 72.1161 5.0994
>
>
>
> Receptor:
>
> Receptor:
>
> Energy Component Average Std. Dev. Std. Err. of Mean
>
> Energy Component Average Std. Dev. Std. Err. of Mean
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> VDWAALS -2279.0229 22.5574 1.5950
>
> VDWAALS -2279.0229 22.5574 1.5950
>
> EEL -23284.9397 65.8095 4.6534
>
> EEL -23284.9397 65.8095 4.6534
>
> EGB -3438.6212 44.9608 3.1792
>
>
>
>
>
> EPB -3484.5218 43.8002 3.0971
>
> ESURF 93.8546 0.9062 0.0641
>
>
>
>
>
> ECAVITY 101.6977 0.5965 0.0422
>
>
> G gas -25563.9626 65.0641 4.6007
>
> G gas -25563.9626 65.0641 4.6007
>
> G solv -3344.7666 44.7765 3.1662
>
>
>
>
>
> G solv -3382.8242 43.7453 3.0933
>
>
> TOTAL -28908.7291 41.1937 2.9128
>
> TOTAL -28946.7868 46.5430 3.2911
>
>
>
> Ligand:
>
> Ligand:
>
> Energy Component Average Std. Dev. Std. Err. of Mean
>
> Energy Component Average Std. Dev. Std. Err. of Mean
>
> -------------------------------------------------------------------------------
>
> -------------------------------------------------------------------------------
>
> VDWAALS -2258.2667 23.3770 1.6530
>
> VDWAALS -2258.2667 23.3770 1.6530
>
> EEL -23248.4845 79.3244 5.6091
>
> EEL -23248.4845 79.3244 5.6091
>
> EGB -3504.8952 59.1518 4.1827
>
>
>
>
>
> EPB -3532.5437 58.4830 4.1354
>
> ESURF 94.7291 0.8840 0.0625
>
>
>
>
>
> ECAVITY 102.5529 0.8162 0.0577
>
>
> G gas -25506.7513 80.1946 5.6706
>
> G gas -25506.7513 80.1946 5.6706
>
> G solv -3410.1661 58.7464 4.1540
>
>
>
>
>
> G solv -3429.9908 58.0774 4.1067
>
>
> TOTAL -28916.9174 44.3756 3.1378
>
> TOTAL -28936.7420 49.1077 3.4724
>
>
>
>
>
>
> -----Original Message-----
> From: Ray Luo, Ph.D. [mailto:ray.luo.uci.edu]
> Sent: Wednesday, August 01, 2012 2:39 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] large difference between MMGBSA and MMPBSA free energy
>
>
>
> What are your total free energies for the complex and the standalone
>
> proteins? Most likely the differences would be much smaller in
>
> percentage term. When computing deltaG, the percentage difference
>
> always go up due to cancellation of significant leading digits in the
>
> free energies.
>
>
>
> Ray
>
>
>
> On Wed, Aug 1, 2012 at 12:26 PM, Kong, Ren <rkong.tmhs.org> wrote:
>
>> Hi,
>
>>
>
>> I used the MMPBSA.py to calculate the GB and PB energy for a system of dimer protein with calcium ions.
>
>> The input is :
>
>> &general
>
>> startframe=1,endframe=2000,
>
>> interval=10,
>
>> receptor_mask=':1-334,:669-674',ligand_mask=':335-668,:675-680'
>
>> /
>
>> &gb
>
>> igb=5, saltcon=0.15,surften=0.005
>
>> /
>
>> &pb
>
>> istrng=0.15,fillratio=4.0,exdi=78.5,scale=0.67
>
>> /
>
>> The final results made me a little confused:
>
>>
>
>> GENERALIZED BORN:
>
>> DELTA G binding = -4.1529 +/- 3.2338 0.2287
>
>> POISSON BOLTZMANN:
>
>> DELTA G binding = -31.0614 +/- 5.3846 0.3807
>
>>
>
>> Why there is such a big difference between GB and PB calculation?
>
>> Which one should be reliable in this case?
>
>>
>
>> Best,
>
>> Ren Kong Ph.D.
>
>> rkong.tmhs.org<mailto:ltsou.tmhs.org>
>
>>
>
>>
>
>> Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNE(r) Magazine's "100 Best Companies to Work For(r)" list seven years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at methodisthealth.com. Follow us at twitter.com/MethodistHosp and www.facebook.com/MethodistHospital. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.
>
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>
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>
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>
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>
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Received on Wed Aug 01 2012 - 15:00:02 PDT
