Dear Amber community!
Recently i have encountered some problems about mm_pbsa. I have done simulation about binding of two ligands (small molecules) in Amber7. then I use mm_pbsa to calculte the free energy of binding. however i got the result(snap_statistics.out) like below:
my question is why the PBCAL energy = 0.00, but i think it is impossible because in the complex (just two small molecules) there are many -OH groups. then i check the m_pbsa.in(below,just part) and my_amber94_delphi.crg(below)however, i cannot find the error!
could you help me to configure out!
Thank you very much:)
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compchem 15% more snap_statistics.out
# COMPLEX RECEPTOR LIGAND
# ----------------------- ----------------------- -----------------------
# MEAN STD MEAN STD MEAN STD
# ======================= ======================= =======================
ELE 54.65 0.00 113.09 0.00 -51.42 0.00
VDW 27.29 0.00 24.45 0.00 21.54 0.00
INT 291.33 0.00 211.65 0.00 79.68 0.00
GAS 373.27 0.00 349.18 0.00 49.80 0.00
PBSUR 5.39 0.00 4.05 0.00 2.30 0.00
PBCAL 0.00 0.00 0.00 0.00 0.00 0.00
PBSOL 5.39 0.00 4.05 0.00 2.30 0.00
PBELE 54.65 0.00 113.09 0.00 -51.42 0.00
PBTOT 378.66 0.00 353.24 0.00 52.09 0.00
GBSUR 7.03 0.00 5.26 0.00 2.93 0.00
GB -16.77 0.00 -13.48 0.00 -5.17 0.00
GBSOL -9.74 0.00 -8.22 0.00 -2.24 0.00
GBELE 37.88 0.00 99.61 0.00 -56.59 0.00
GBTOT 363.53 0.00 340.97 0.00 47.56 0.00
# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -7.01 0.00 (BECAUSE OF I JUST USE ONLY ONE SNAPSHOT ,So STD = 0.00)
VDW -18.70 0.00
INT 0.00 0.00
GAS -25.71 0.00
PBSUR -0.96 0.00
PBCAL 0.00 0.00
PBSOL -0.96 0.00
PBELE -7.01 0.00
PBTOT -26.67 0.00
GBSUR -1.16 0.00
GB 1.88 0.00
GBSOL 0.72 0.00
GBELE -5.14 0.00
GBTOT -24.99 0.00
PREFIX snap
PATH ../1_snap/
COMPLEX 1
RECEPTOR 1
LIGAND 1
#
COMPT ../com.top
RECPT ../ligand1.top
LIGPT ../ligand2.top
#
GC 0
AS 0
DC 0
#
MM 1
GB 1
PB 1
MS 1
#
NM 0
-------
FOCUS 0
INDI 1.0
EXDI 80.0
PERFIL 80.0
SCALE 2
LINIT 1000
BNDCON 4
CHARGE ../my_amber94_delphi.crg
SIZE ../my_parse_delphi.siz
#
SURFTEN 0.00542
SURFOFF 0.092
_______
#
IGB 4
SALTCON 0.00
EXTDIEL 80.0
#
SURFTEN 0.0072
SURFOFF 0.00
#
################################################################################
.MS
#
# Molsurf parameters
#
# PROBE - Radius of the probe sphere used to calculate the SAS.
# RADII - Name of the radii file.
#
PROBE 1.4
RADII ../atmtypenumbers
#
#################################################################################
.PROGRAMS
#
# Program executables
DELPHI /disk8/yxu/program/amber7/delphi/delphi
#
________________________________________________________________________________________
compchem 27% more amber94_delphi.crg_backup
!Amber parm94 charges
atom__resnumbc_charge_
O11 ZAO -0.713
H26 ZAO 0.433
C17 ZAO 0.287
C16 ZAO 0.317
C14 ZAO 0.077
O10 ZAO -0.682
H25 ZAO 0.451
H21 ZAO 0.075
O12 ZAO -0.666
H27 ZAO 0.418
H23 ZAO 0.040
H24 ZAO 0.087
C15 ZAO 0.145
C18 ZAO -0.445
H28 ZAO 0.122
H29 ZAO 0.122
H30 ZAO 0.122
H22 ZAO 0.065
O9 ZAO -0.383
C13 ZAO 0.163
H20 ZAO 0.135
O2 ZAO -0.451
C3 ZAO 0.315
H3 ZAO 0.082
C2 ZAO 0.051
O3 ZAO -0.716
H6 ZAO 0.476
H2 ZAO 0.075
C1 ZAO 0.070
O5 ZAO -0.473
C11 ZAO 0.298
O6 ZAO -0.489
C9 ZAO 0.513
C7 ZAO 0.071
C8 ZAO 0.168
C10 ZAO 0.203
O13 ZAO -0.725
H31 ZAO 0.481
H13 ZAO 0.079
O8 ZAO -0.711
H19 ZAO 0.441
H11 ZAO 0.070
O7 ZAO -0.709
H18 ZAO 0.448
H10 ZAO 0.094
C12 ZAO -0.509
H15 ZAO 0.140
H16 ZAO 0.140
H17 ZAO 0.140
H12 ZAO 0.021
H14 ZAO 0.129
H1 ZAO 0.085
C5 ZAO 0.415
C6 ZAO 0.147
O4 ZAO -0.719
H9 ZAO 0.449
H7 ZAO 0.030
H8 ZAO 0.030
H5 ZAO 0.027
O1 ZAO -0.607
C4 ZAO 0.393
H4 ZAO 0.033
O15 ZAO -0.563
C21 ZAO 0.529
C22 ZAO -0.354
H37 ZAO 0.122
H38 ZAO 0.122
H36 ZAO -0.008
C20 ZAO -0.062
H34 ZAO 0.063
H35 ZAO 0.063
C19 ZAO -0.352
H32 ZAO 0.081
H33 ZAO 0.081
C28 ZAO 0.260
C37 ZAO -0.353
H56 ZAO 0.088
H57 ZAO 0.088
H58 ZAO 0.088
C23 ZAO -0.079
C24 ZAO -0.235
H39 ZAO 0.141
C25 ZAO -0.136
H40 ZAO 0.061
H41 ZAO 0.061
C26 ZAO 0.104
H42 ZAO 0.031
C27 ZAO 0.079
H43 ZAO 0.006
C29 ZAO -0.096
H44 ZAO 0.037
H45 ZAO 0.037
C30 ZAO -0.245
H46 ZAO 0.045
H47 ZAO 0.045
C31 ZAO 0.433
C36 ZAO -0.336
H53 ZAO 0.065
H54 ZAO 0.065
H55 ZAO 0.065
C32 ZAO -0.081
H48 ZAO 0.010
C33 ZAO -0.238
H49 ZAO 0.071
H50 ZAO 0.071
C34 ZAO 0.279
O14 ZAO -0.453
H51 ZAO 0.021
C35 ZAO -0.160
H52 ZAO 0.040
C38 ZAO 0.056
C44 ZAO -0.415
H68 ZAO 0.106
H69 ZAO 0.106
H70 ZAO 0.106
H59 ZAO 0.039
C39 ZAO 0.415
C40 ZAO -0.041
H60 ZAO 0.023
H61 ZAO 0.023
C41 ZAO 0.028
H62 ZAO -0.003
H63 ZAO -0.003
C42 ZAO -0.030
H64 ZAO 0.012
H65 ZAO 0.012
C43 ZAO 0.171
H66 ZAO 0.024
H67 ZAO 0.024
O16 ZAO -0.436
C19 MOL -0.272
H27 MOL 0.064
H28 MOL 0.064
H29 MOL 0.064
C10 MOL 0.370
C1 MOL -0.240
H2 MOL 0.054
H3 MOL 0.054
C2 MOL -0.078
H4 MOL 0.064
H5 MOL 0.064
C3 MOL 0.409
O1 MOL -0.769
H1 MOL 0.444
H6 MOL -0.006
C4 MOL -0.300
H7 MOL 0.108
H8 MOL 0.108
C5 MOL -0.156
C6 MOL -0.213
H9 MOL 0.133
C7 MOL -0.107
H10 MOL 0.055
H11 MOL 0.055
C8 MOL 0.024
H12 MOL 0.041
C9 MOL -0.026
H13 MOL 0.015
C11 MOL -0.105
H14 MOL 0.029
H15 MOL 0.029
C12 MOL -0.110
H16 MOL 0.016
H17 MOL 0.016
C13 MOL 0.366
C18 MOL -0.426
H24 MOL 0.091
H25 MOL 0.091
H26 MOL 0.091
C14 MOL 0.026
H18 MOL 0.010
C15 MOL -0.176
H19 MOL 0.043
H20 MOL 0.043
C16 MOL -0.091
H21 MOL 0.036
H22 MOL 0.036
C17 MOL -0.040
H23 MOL -0.005
C20 MOL 0.131
C21 MOL -0.316
H31 MOL 0.069
H32 MOL 0.069
H33 MOL 0.069
H30 MOL 0.000
C22 MOL -0.026
H34 MOL 0.000
H35 MOL 0.000
C23 MOL 0.075
H36 MOL -0.003
H37 MOL -0.003
C24 MOL -0.279
H38 MOL 0.066
H39 MOL 0.066
C25 MOL 0.391
C27 MOL -0.431
H44 MOL 0.099
H45 MOL 0.099
H46 MOL 0.099
H40 MOL -0.031
C26 MOL -0.431
H41 MOL 0.099
H42 MOL 0.099
H43 MOL 0.099
linfu
linfu3200.mail.sioc.ac.cn
2006-01-08
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Received on Tue Jan 10 2006 - 06:10:06 PST
