Dear amber users,
in amber/src/mm_pbsa/Examples/03_MMPBSA_Binding
Amber8: GBSOL 1297.29 14.91
Amber7: GBSOL 1306.06 13.89
I find the differnce
Amber7:
# IGB - Switches between Tsui's GB (1), Onufriev's GB (2),
# Jayaram's et al. GB (3) or Jayaram's et al. MGB (4).
IGB 4
SALTCON 0.00
EXTDIEL 80.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.MS
#
# Molsurf parameters
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# RADII - Name of the radii file.
#
PROBE 1.4
RADII ../atmtypenumbers
Amber8:
.GB
# IGB - Switches between Tsui¨s GB (1) and Onufriev¨s GB (2, 5).
# GBSA - Switches between LCPO (1) and ICOSA (2) method for SASA calc.
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.MS
#
# Molsurf parameters (this section is only relevant if MS = 1 above)
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# Since Bondi radii are already augmented by 1.4A, PROBE should be 0.0
#
PROBE 0.0
Why amber8 changes so much? Which is better?
Thanks!
regards!
Xiao He
hx.itcc.nju.edu.cn
2004-10-15
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Received on Fri Oct 15 2004 - 12:53:00 PDT
