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>
>
>
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Received on Wed Aug 01 2012 - 14:00:03 PDT
