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

From: Ray Luo, Ph.D. <>
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.


On Wed, Aug 1, 2012 at 12:26 PM, Kong, Ren <> wrote:
> Hi,
> I used the 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:
> DELTA G binding = -4.1529 +/- 3.2338 0.2287
> 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.
> Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 13 specialties. Named to FORTUNEŽ Magazine's "100 Best Companies to Work ForŽ" list seven years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at Follow us at and ***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.
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Aug 01 2012 - 13:00:03 PDT
Custom Search