See my reply below ...
Jeffrey wrote:
> .PB
> #
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 2
> LINIT 10000
> PRBRAD 1.4
> ISTRNG 0.0
> RADIOPT 0
> NPOPT 1
> cavity_surften 0.00542
> cavity_offset 0.92
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> #
> ################################################################################
> .MM
> #
> DIELC 1.0
> #
> #
> .GB
> #
> #
> IGB 2
> GBSA 1
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> #
> SURFTEN 0.0072
> SURFOFF 0.00
> #
> #
> .MS
> #
> PROBE 0.0
> #
> .PROGRAMS
> ------------------------------
> In this script we set parameters cavity_surften = 0.00542, cavity_offset = 0.92 and MS =0.
> Then the nonpolar solvation free energy will be computed by Gnp = cavity_surften*SASA + cavity_offset.
> But in the files pbsa_com.in, pbsa_rec.in and pbsa_lig.in, the following parameters are found:
> ----
> ...
> &pb
> ...
> cavity_surften = 0.0072, cavity_offset = 0.00,
> npbverb= 1
> &end
> ----
> where cavity_surften = 0.0072 and cavity_offset = 0.00 are used.
> While in the output file mmpbsa-binding.out(mm_pbsa.pl mmpbsa-binding.inp > mmpbsa-binding.out),
> the following parameters are found:
> --------
> =>> Values of global variables
> TEMP = 300
> R = 8.314
> gammaP = 1
> betaP = 0
> gammaG = 0.0072
> betaG = 0.000
> ------------------------
> Why the values of cavity_surften and cavity_offset are different in the input script (mmpbsa-binding.inp),
> the pbsa_*.in files, and the output file ( mmpbsa-binding.out) ? I am really confused...
> Thanks for the time.
>
Because you set
#
SURFTEN 0.0072
SURFOFF 0.00
For both PB and GB calculations.
The options
cavity_surften 0.00542
cavity_offset 0.92
are not recognized by the mmpbsa script. In general the mmpbsa options
are NOT keywords in the input file. This is a very unfortunate fact for
beginners of mmpbsa.
A general suggestion for beginners is to go through the mmpbsa
calculations automated by the script BY HAND at least once to understand
the flow of data.
All the best,
Ray
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Received on Thu Mar 18 2010 - 10:30:05 PDT
