Dear Amber users,
I am running MMPBSA calcuations for 100sps, my input file for that is:
#
# Input parameters for mm_pbsa.pl
#
#
################################################################################
#
VERBOSE 0
PARALLEL 0
#
PREFIX L
PATH ./
START 1
STOP 1
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
#
################################################################################
#
PROC 2
REFE 0
INDI 1.0
EXDI 80.0
SCALE 2
LINIT 1000
PRBRAD 1.4
ISTRNG 0.0
RADIOPT 0
INP 1
#
SURFTEN 0.04356
SURFOFF -1.008
#
IVCAP 0
CUTCAP -1.0
XCAP 0.0
YCAP 0.0
ZCAP 0.0
#
################################################################################
.MM
#
# MM parameters (this section is only relevant if MM = 1 above)
#
# The following parameters are passed to sander.
# For further details see the sander documentation.
#
# DIELC - Dielectricity constant for electrostatic interactions.
# Note: This is not related to GB calculations.
#
DIELC 1.0
#
################################################################################
# the desolvation according to Gnp = SURFTEN * SASA + SURFOFF.
#
IGB 5
GBSA 1
SALTCON 0.00
EXTDIEL 80.0
INTDIEL 1.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.MS
#
# Molsurf parameters (this section is only relevant if MS = 1 above)
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# In general, since Bondi radii are already augmented by 1.4A,
# PROBE should be 0.0
# In IVCAP = 1 or 5, the solvent excluded surface is required for
# calculating the cavity contribution. Bondi radii are not
# augmented in this case and PROBE should be 1.4.
#
PROBE 0.0
#
################################################################################
but the energy that I am getting is huge ...
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE -10841.03 101.25 -10410.47 96.18 -190.08 17.55
VDW -1543.33 28.21 -1466.58 27.14 195120.40 4894.33
INT 8334.19 51.25 8119.96 49.62 168750.44 12093.84
GAS -4050.18 109.39 -3757.09 105.02 363680.75 13158.43
PBSUR 927.79 6.78 927.94 6.33 77.73 1.32
PBCAL -6405.31 89.46 -6405.69 83.25 -437.07 13.88
PBSOL -5477.52 87.33 -5477.76 80.88 -359.33 14.13
PBELE -17246.34 36.97 -16816.16 36.62 -627.15 9.25
PBTOT -9527.70 53.87 -9234.85 52.03 363321.42 13157.67
GBSUR 153.52 1.12 153.54 1.05 13.02 0.22
GB -3611.13 96.16 -3775.40 90.77 -310.76 13.24
GBSOL -3457.61 95.80 -3621.85 90.41 -297.75 13.26
GBELE -14452.16 62.85 -14185.86 58.91 -500.85 11.48
GBTOT -7507.79 78.59 -7378.94 75.06 363383.00 13157.15
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -240.48 140.75
VDW -195197.15 4894.48
INT -168536.20 12094.05
GAS -363973.84 13159.30
PBSUR -77.88 9.37
PBCAL 437.45 122.98
PBSOL 359.57 119.87
PBELE 196.97 52.85
PBTOT -363614.26 13157.88
GBSUR -13.04 1.55
GB 475.03 132.90
GBSOL 461.99 132.39
GBELE 234.55 86.90
GBTOT -363511.84 13157.60
when I am running MMPBSA.py for the same snapshots the energies are :
Differences (Complex - Receptor - Ligand):
Energy Component Average Std. Dev. Std. Err. of Mean
-------------------------------------------------------------------------------
VDWAALS -86.1604 4.7220 0.4722
EEL -322.6536 22.3014 2.2301
EGB 357.6727 20.9844 2.0984
ESURF -12.0810 0.4190 0.0419
DELTA G gas -408.8140 20.9551 2.0955
DELTA G solv 345.5916 20.9989 2.0999
DELTA G binding = -63.2223 +/- 3.8132 0.3813
What is the problem here? For MMPBSA.py I am not able to get PB energy, with GB there is no problem...
Thank you in advance for any suggestions,
/Urszula
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 31 2012 - 22:30:02 PST
