Dear all,
I wonder if there is a difference in GB calculations between AMBER7 and
AMBER8.
Indeed I remarked a difference when I calculate the energy of my
structures when I am running
MMGBSA calculations. The difference is always around 4 kcal/mol for
every snapshot for GB energies.
Here are my results :
with AMBER 7 :
# MEAN STD
# =======================
ELE -6636.65 68.47
VDW -700.80 26.89
INT 4340.43 42.15
GAS -2997.02 76.28
GBSUR 61.49 1.23
GB -3470.58 56.05
GBSOL -3409.10 55.62
GBELE -10107.23 27.20
GBTOT -6406.12 40.64
with AMBER8 :
# MEAN STD
# =======================
ELE -6636.65 68.47
VDW -700.80 26.89
INT 4340.43 42.15
GAS -2997.02 76.28
PBSUR 61.49 1.23
PBCAL -3442.74 56.73
PBSOL -3381.26 56.15
PBELE -10079.39 36.92
PBTOT -6378.28 43.33
GBSUR 61.49 1.23
GB -3474.91 56.07
GBSOL -3413.43 55.65
GBELE -10111.56 27.17
GBTOT -6410.45 40.63
As can be seen, everything is identical except for GB energies.
The input scripts for sander which are generated by mm_pbsa.pl are the
same.
Does anyone have any suggestion ?
Thanks in advance,
Yours sincerely,
Fabien
--
__________________________________________________________________
Fabien Cailliez Tel : 01 58 41 51 63
Laboratoire de Biochimie Théorique e-mail : cailliez.ibpc.fr
IBPC 13, rue Pierre et Marie Curie
75005 Paris
__________________________________________________________________
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Received on Tue Jan 18 2005 - 14:53:01 PST
