MMPBSA calculation input file
&general
startframe=1, endframe=200, interval=1,
verbose=2,
strip_mask=:200-204:206-8051
/
&pb
sander_apbs=1, indi=1,
/
receptor is 1-198
ligand is 199
water is 205
last (water) residue is 8051
Maximum number of minimization cycles reached.
And the energy problem is not only for one but all snapshots:
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.3918E+08 6.0401E+04 1.8073E+05 C3 13
BOND = ************* ANGLE = 8568.5539 DIHED =
324.6412
VDWAALS = 1502.4033 EEL = 6.2939 EPB =
-978.2764
1-4 VDW = -0.0005 1-4 EEL = -4.6667 RESTRAINT =
0.0000
ENPOLAR = 40.9749
minimization completed, ENE= 0.13917949E+09 RMS= 0.604013E+05
minimizing coord set # 27
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.5284E+08 6.1880E+04 1.9712E+05 O 71
BOND = ************* ANGLE = 7841.0018 DIHED =
271.8407
VDWAALS = -0.0418 EEL = -37.5258 EPB =
-961.8115
1-4 VDW = -0.0027 1-4 EEL = 20.7267 RESTRAINT =
0.0000
ENPOLAR = 41.0488
minimization completed, ENE= 0.15284473E+09 RMS= 0.618804E+05
minimizing coord set # 28
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.4857E+08 6.3355E+04 2.1190E+05 C3 13
BOND = ************* ANGLE = 9474.7097 DIHED =
297.6169
VDWAALS = -0.0237 EEL = 0.0768 EPB =
-986.7307
1-4 VDW = -0.0000 1-4 EEL = 0.9346 RESTRAINT =
0.0000
ENPOLAR = 41.2883
minimization completed, ENE= 0.14856890E+09 RMS= 0.633553E+05
minimizing coord set # 29
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.1970E+08 5.5393E+04 1.7757E+05 S1 7
BOND = ************* ANGLE = 8193.2024 DIHED =
289.4883
VDWAALS = -0.1859 EEL = -59.7277 EPB =
-912.0416
1-4 VDW = -0.0007 1-4 EEL = -4.2525 RESTRAINT =
0.0000
ENPOLAR = 40.8737
minimization completed, ENE= 0.11969814E+09 RMS= 0.553932E+05
minimizing coord set # 30
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 1.5478E+08 6.6942E+04 2.3440E+05 C20 55
BOND = ************* ANGLE = 10027.3003 DIHED =
265.0834
VDWAALS = -0.0028 EEL = -5.4611 EPB =
-974.1943
1-4 VDW = -0.0001 1-4 EEL = 4.8587 RESTRAINT =
0.0000
ENPOLAR = 41.4313
minimization completed, ENE= 0.15478438E+09 RMS= 0.669419E+05
minimizing coord set # 31
--
Oliver Kuhn, Department of Bioinformatics,
Center for Medical Biotechnology, University of Duisburg-Essen,
Universitätsstr. 1-5, 45141 Essen, Germany
phone +49 201 183-3121, oliver.kuhn.uni-due.de
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Received on Mon May 16 2011 - 13:30:04 PDT
