AMBER Archive (2006)

Subject: RE: AMBER: MM-PBSA problem

From: Ray Luo (rluo_at_uci.edu)
Date: Fri Dec 01 2006 - 15:51:52 CST

Which Amber distribution are you using?

 

Ray

 

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
vanessa wai
Sent: Thursday, November 30, 2006 5:27 PM
To: amber_at_scripps.edu
Subject: AMBER: MM-PBSA problem

 

Dear Amber users,

Hello there. I encounter a problem in interpreting the results that I got
from MM-PBSA calculation on binding free energy of ligand to my protein.
PBTOT that I got (please refer below) from the calculation is very very
positive (almost impossible), however GBTOT values looks like a more
acceptable value as compared to experimental value. Any ideas on how this
could happen? Any ideas are welcome.

Thanks a lot and hope to hear from you all soon.

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE - 5.72 16.86
VDW -87.34 11.22
INT 0.00 0.00
GAS -93.06 13.61
PBSUR -7.00 0.20
PBCAL 718.76 210.20
PBSOL 711.76 210.01
PBELE 713.04 222.37
PBTOT 618.70 215.23
GBSUR -10.08 0.29
GB 81.72 13.44
GBSOL 71.64 13.63
GBELE 76.00 5.44
GBTOT -21.41 11.30

Best regards,
Vanessa

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