AMBER Archive (2006)

Subject: AMBER: about mmpbsa

From: linfu (linfu3200_at_mail.sioc.ac.cn)
Date: Mon Jan 09 2006 - 19:17:15 CST

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:)

BEST WISHES

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_at_mail.sioc.ac.cn
　　　　　　　　　　2006-01-08
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