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® Magazine's "100 Best Companies to Work For®" 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.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 01 2012 - 12:30:03 PDT
