[AMBER] MMPBSA calculation

From: Jeffrey <jeffry20072008.yahoo.cn>
Date: Thu, 18 Mar 2010 20:23:36 +0800

Dear AMBER users,
I am going to calculate the binding free energy btw a protein (receptor) and a small molecule (ligand) by using the MMPBSA module in AMBER10.
The input file used for input is as follows:
------------------------------------------- mmpbsa-binding.inp
# Input parameters for mm_pbsa.pl
.GENERAL
#
PREFIX snapshot
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ./comp.prmtop
RECPT ./rec.prmtop
LIGPT ./lig.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 1
MS 0
#
NM 0
#
##################################################################
.DECOMP
#
DCTYPE 2
#
COMREC 1-304
COMLIG 305
COMPRI 1-305
RECRES 1-304
RECPRI 1-304
RECMAP 1-304
LIGRES 1
LIGPRI 1
LIGMAP 305
#
.PB
#
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 10000
ISTRNG 0.0
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.
Jeffrey Yang
---DICP,CAS
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```
Received on Thu Mar 18 2010 - 05:30:02 PDT
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