Re: [AMBER] large difference between MMGBSA and MMPBSA free energy

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Wed, 1 Aug 2012 12:38:44 -0700

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 - 13:00:03 PDT