[AMBER] large difference between MMGBSA and MMPBSA free energy

From: Kong, Ren <rkong.tmhs.org>
Date: Wed, 1 Aug 2012 14:26:02 -0500


I used the MMPBSA.py to calculate the GB and PB energy for a system of dimer protein with calcium ions.
The input is :
   igb=5, saltcon=0.15,surften=0.005
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?

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 FORTUNEĀ® Magazine's "100 Best Companies to Work ForĀ®" 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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Received on Wed Aug 01 2012 - 12:30:03 PDT
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