Hello All,
I am trying to calculate binding free energy for DNA
qudruplex ligand interaction but I am getting positive
Binding energy. I did 14 ns dynamics and RMS value of
the complex is arround 1.7. But I am not
understanding why delta G is comming positive. The
result of mmpbsa is given below.
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -44.73 13.15
VDW -45.72 1.74
INT -0.00 0.00
GAS -90.46 12.81
GBSUR -3.03 0.08
GB 108.72 16.04
GBSOL 105.68 15.99
GBELE 63.98 4.93
GBTOT 15.23 4.84
m_pbsa.in script is as follows.
*****************************************************
PREFIX t
PATH ../01_GenerateSnapshots/
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../comp.top
RECPT ../recp.top
LIGPT ../lig.top
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 0
MS 1
#
NM 0
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2.0
LINIT 1000
PRBRAD 1.4
#
RADIOPT 0
DIELC 1.0
IGB 2
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.005
SURFOFF 0.00
PROBE 0.0
If someone may tell me the probable reason of this
high binding energy, I shall be highly thankful to
him.
saurabh
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Received on Wed Feb 07 2007 - 06:07:22 PST
