AMBER Archive (2006)

Subject: AMBER: errors in mm_pbsa.in in AMBER 8 mannul ?

From: tonglei (xbcdnana_at_gmail.com)
Date: Tue Apr 04 2006 - 08:10:59 CDT


Dear Pro Gohlke:

I have a question about the mmpbsa input files in the examples.

In the J Comput Chem 25,238-250,2004 there are some conclusions about GB
models "Tsui et al. ("vtGB"), Onufriev et al. ("aoGB"), and Jayaramet al. ("
MGB")." And the values of SURFTEN and SURFOFF are "0.0072 kcal mol-1 _2 and
0 kcal mol/1,respectively, in connection with the MGB model, and to
0.005kcal mol-1 _2 and 0 kcal mol-1, respectively, in connection with the
vtGB and aoGB models."

 However, in mm_pbsa.in of the Amber 8 mannul and the examples, especially
the GB term

There is not the Jayaramet al. ("MGB") at all ,and when the IGB=2 (refers to
the Onufriev's GB ) aoGB, I think the SURFTEN should be 0.005kcal
mol-1 _2, but
here it is 0.0072 (MGB)

And from the input files, there isn't the MGB options. Is there anything
wrong ?

# GB parameters (this section is only relevant if GB = 1 above)

#

# The first group of the following parameters are passed to sander.

# For further details see the sander documentation.

#

# * **IGB - Switches between Tsui's GB (1), Onufriev's GB (2, 5).*

# GBSA - Switches between LCPO (1) and ICOSA (2) method for SASA calc.

# Decomposition only works with ICOSA.

# SALTCON - Concentration (in M) of 1-1 mobile counterions in solution.

# EXTDIEL - Dielectricity constant for the solvent.

# INTDIEL - Dielectricity constant for the solute

#

# SURFTEN / SURFOFF - Values used to compute the nonpolar contribution Gnp
to

# the desolvation according to Gnp = SURFTEN * SASA +
SURFOFF.

#
IGB 2

SALTCON 0.1

EXTDIEL 80.0

INTDIEL 1.0

#
SURFTEN 0.0072

SURFOFF 0.00

What about this ?

 Thank you

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