Dear all,
I'm trying to calculate binding energy between glucose molecule and pure
water by using AMBER 11 package. What I'm getting in trouble is GBtot has
positive value (delta section in snap_statistics.out file). As you know,
water interacts with glucose strongly, which means Binding energy should be
negative value.
There is single glucose molecule in TIP3P water box (625 molecules). and
this simulation is 10ns simulation under NVT condition.
Here belows are scripts which I've used,
<<Taking snapshot>>
PREFIX snap_
PATH ./
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
GC 1
AS 0
DC 0
#
MM 0
GB 0
PB 0
MS 0
#
NM 0
BOX YES
NTOTAL 1899
NSTART 1
NSTOP 1
NFREQ 1
#
NUMBER_LIG_GROUPS 1
LSTART 1
LSTOP 24
NUMBER_REC_GROUPS 1
RSTART 25
RSTOP 1899
.TRAJECTORY
TRAJECTORY ./md_9999.x
<MM_PBSA_GB>>
PREFIX snap_
PATH ./snapshot
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT Lwatall.prmtop
RECPT Lwatrest.prmtop
LIGPT Lwat03.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 0
MS 1
#
NM 0
.GB
IGB 2
GBSA 1
SALTCON 0
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
.MS
PROBE 0.0
.MM
DIELC 1.0
.PB
#PROC 2
#REFE 0
#INDI 1.0
#EXDI 80.0
#SCALE 2
#LINIT 1000
#PRBRAD 1.4
#ISTRNG 0.0
#RADIOPT 0
#NPOPT 1
#CAVITY_SURFTEN 0.0072
#CAVITY_OFFSET 0.00
#SURFTEN 0.0072
#SURFOFF 0.00
<Result>
DELTA
# -----------------------
# MEAN STD
# =======================
ELE -21.06 11.89
VDW -5.59 0.00
INT 0.00 0.00
GAS -26.65 11.89
GBSUR 0.00 0.00
GB 40.26 22.94
GBSOL 40.26 22.94
GBELE 19.20 11.06
*GBTOT 13.61 11.06*
*
*
Could anyone give me an advice to figure it out ?
Thanks you in advance.
Hoshin Kim
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Received on Thu Mar 24 2011 - 18:30:02 PDT
