Dear Amber users,
Here are the results of the binding energy calculated by python and perl
mm/pbsa respectively, and also the input files are showed here.
the input file for calculation of perl version:
.GENERAL
VERBOSE 0
PARALLEL 8
#
PREFIX snapshot
PATH ../snapshots/
START 1
STOP 400
OFFSET 1
#
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../com.prmtop
RECPT ../rec.prmtop
LIGPT ../lig.prmtop
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 1
MS 1
#
NM 0
#
################################################################################
.PB
#
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.10
RADIOPT 1
INP 1
#
SURFTEN 0.00542
SURFOFF -1.008
#
IVCAP 0
CUTCAP -1.0
XCAP 0.0
YCAP 0.0
ZCAP 0.0
#
################################################################################
.MM
#
DIELC 1.0
#
################################################################################
.GB
#
IGB 5
GBSA 2
SALTCON 0.10
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
################################################################################
.MS
PROBE 0.0
################################################################################
.PROGRAMS
# Additional program executables can be defined here
################################################################################
and here are the results:
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -269.04 11.21
VDW -63.58 4.63
INT -0.00 0.01
GAS -332.63 10.49
PBSUR -6.10 0.26
PBCAL 290.70 9.67
PBSOL 284.60 9.64
PBELE 21.66 6.73
PBTOT -48.03 5.32
GBSUR -9.44 0.34
GB 204.37 23.16
GBSOL 194.93 23.20
GBELE -64.67 22.01
GBTOT -137.70 22.03
For the python case, the input file is:
&general
startframe=1, endframe=400, interval=1,
verbose=1, keep_files=1,
/
&gb
igb=5, saltcon=0.10, surften=0.0072, surfoff=0.00,
/
&pb
indi=1.0, exdi=80.0, scale=2.0, linit=1000, prbrad=1.4,
inp=1, istrng=0.10, cavity_surften=0.00542, cavity_offset=-1.008,
fillratio=4.0,
/
and the results of the calculation are:
GB:
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -63.5848 4.6231
0.2312
EEL -269.0419 11.1926
0.5596
EGB 259.9393 9.7870
0.4893
ESURF -8.0095 0.3432
0.0172
DELTA G gas -332.6283 10.4807
0.5240
DELTA G solv 251.9298 9.8082
0.4904
DELTA G binding = -80.6986 +/- 5.1168
0.2558
PB:
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
VDWAALS -63.5848 4.6231
0.2312
EEL -269.0419 11.1926
0.5596
EPB 284.6789 8.9675
0.4484
ECAVITY -6.2191 0.2638
0.0132
DELTA G gas -332.6283 10.4807
0.5240
DELTA G solv 278.4598 8.9624
0.4481
DELTA G binding = -54.1686 +/- 4.8905
0.2445
By comparision, we can see that there is a big difference, which is mainly
generated by the solvation free energy. The same situation also exists in
another case. From the input files, I tried to choose the same parameters,
but... So how should I treat the two different results, or how should I
reset the parameters? Thanks very much!
--
Best Regards,
Qinghua
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Received on Fri Dec 16 2011 - 14:30:02 PST
