This is my input file:
Input file for running PB and GB
&general
endframe=50, verbose=2,
/
&gb
igb=2, saltcon=0.300
/
&pb
istrng=0.300,
/
I tried both single and three trajectory protocol, the GB results were OK, but I
cann't get PB results.
This is the_MMPBSA_complex_pb.mdout file:
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| Run on 05/19/2011 at 23:35:27
[-O]verwriting output
File Assignments:
| MDIN: _MMPBSA_pb.mdin
| MDOUT: _MMPBSA_complex_pb.mdout
|INPCRD: _MMPBSA_dummycomplex.inpcrd
| PARM: com_vac.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: _MMPBSA_complex.mdcrd
|
Here is the input file:
File generated by MMPBSA.py
&cntrl
ntb=0, cut=999.0, nsnb=99999,
imin=5, maxcyc=0, cutcap=-1, xcap=0,
ycap=0, zcap=0, idecomp=0, ntpr=1,
ivcap=0, ntmin=2, igb=10, ipb=1, inp=1,
/
&pb
dbfopt=1, epsin=1, epsout=80, istrng=300.0,
radiopt=0, sprob=1.4, space=0.5, maxitn=1000, npopt=1
cavity_surften=0.00542, cavity_offset=-1.008,
fillratio=4,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 04/26/11 Time = 21:26:42
NATOM = 21706 NTYPES = 14 NBONH = 10721 MBONA = 11256
NTHETH = 24249 MTHETA = 15357 NPHIH = 47150 MPHIA = 38843
NHPARM = 0 NPARM = 0 NNB = 119955 NRES = 1435
NBONA = 11256 NTHETA = 15357 NPHIA = 38843 NUMBND = 41
NUMANG = 89 NPTRA = 42 NATYP = 28 NPHB = 0
IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are H(N)-modified Bondi radii
(mbondi2)
| Memory Use Allocated
| Real 1455456
| Hollerith 66555
| Integer 1156608
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 16148 kbytes
| Note: 1-4 EEL scale factors were NOT found in the topology file.
| Using default value of 1.2.
| Note: 1-4 VDW scale factors were NOT found in the topology file.
| Using default value of 2.0.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 5, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 10, nsnb = 99999
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 0, ncyc = 10, ntmin = 2
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
trajectory generated by ptraj
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
trajectory generated by ptraj
minimizing coord set # 1
SA Bomb in sa_arc(): Allocates aborted 0 5014
5014 0 0
This is the _MMPBSA_receptor_pb.mdout file:
-------------------------------------------------------
Amber 11 SANDER 2010
-------------------------------------------------------
| Run on 05/19/2011 at 19:15:19
[-O]verwriting output
File Assignments:
| MDIN: _MMPBSA_pb.mdin
| MDOUT: _MMPBSA_receptor_pb.mdout
|INPCRD: _MMPBSA_dummyreceptor.inpcrd
| PARM: fab_vac.prmtop
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
| MTMD: mtmd
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: _MMPBSA_receptor.mdcrd
|
Here is the input file:
File generated by MMPBSA.py
&cntrl
ntb=0, cut=999.0, nsnb=99999,
imin=5, maxcyc=0, cutcap=-1, xcap=0,
ycap=0, zcap=0, idecomp=0, ntpr=1,
ivcap=0, ntmin=2, igb=10, ipb=1, inp=1,
/
&pb
dbfopt=1, epsin=1, epsout=80, istrng=300.0,
radiopt=0, sprob=1.4, space=0.5, maxitn=1000, npopt=1
cavity_surften=0.00542, cavity_offset=-1.008,
fillratio=4,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 04/26/11 Time = 21:29:53
NATOM = 13486 NTYPES = 14 NBONH = 6650 MBONA = 7014
NTHETH = 15078 MTHETA = 9570 NPHIH = 29324 MPHIA = 24320
NHPARM = 0 NPARM = 0 NNB = 74650 NRES = 906
NBONA = 7014 NTHETA = 9570 NPHIA = 24320 NUMBND = 41
NUMANG = 89 NPTRA = 42 NATYP = 28 NPHB = 0
IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
NCOPY = 0
Implicit solvent radii are H(N)-modified Bondi radii
(mbondi2)
| Memory Use Allocated
| Real 904437
| Hollerith 41366
| Integer 727818
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 10070 kbytes
| Note: 1-4 EEL scale factors were NOT found in the topology file.
| Using default value of 1.2.
| Note: 1-4 VDW scale factors were NOT found in the topology file.
| Using default value of 2.0.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
General flags:
imin = 5, nmropt = 0
Nature and format of input:
ntx = 1, irest = 0, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 1, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 0, ntwv = 0, ntwe = 0
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 10, nsnb = 99999
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 999.00000, intdiel = 1.00000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Energy minimization:
maxcyc = 0, ncyc = 10, ntmin = 2
dx0 = 0.01000, drms = 0.00010
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
trajectory generated by ptraj
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 0
--------------------------------------------------------------------------------
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
trajectory generated by ptraj
minimizing coord set # 1
Total surface charge -13.8364
Reaction field energy -8431.8801
Cavity solvation energy 226.6606
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3838E+04 1.8128E+01 1.1877E+02 C 7444
BOND = 4666.2049 ANGLE = 7011.3192 DIHED = 9404.8492
VDWAALS = -5664.3766 EEL = -62851.5837 EPB = -8431.7922
1-4 VDW = 3032.5858 1-4 EEL = 38768.1472 RESTRAINT = 0.0000
ECAVITY = 226.6606 EDISPER = 0.0000
minimization completed, ENE= -.13837985E+05 RMS= 0.181279E+02
minimizing coord set # 2
Total surface charge -13.7689
Reaction field energy -8533.6475
Cavity solvation energy 226.7245
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3983E+04 1.7922E+01 1.1415E+02 C 1826
BOND = 4635.3863 ANGLE = 6975.2422 DIHED = 9355.6731
VDWAALS = -5668.9391 EEL = -62671.1759 EPB = -8533.8157
1-4 VDW = 2991.4301 1-4 EEL = 38706.9325 RESTRAINT = 0.0000
ECAVITY = 226.7245 EDISPER = 0.0000
minimization completed, ENE= -.13982542E+05 RMS= 0.179219E+02
minimizing coord set # 3
Total surface charge -13.7835
Reaction field energy -8448.5982
Cavity solvation energy 225.9911
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3913E+04 1.8095E+01 1.2042E+02 N 1089
BOND = 4664.2361 ANGLE = 6994.4388 DIHED = 9372.8187
VDWAALS = -5655.9036 EEL = -62733.9492 EPB = -8448.3772
1-4 VDW = 2975.9379 1-4 EEL = 38692.0901 RESTRAINT = 0.0000
ECAVITY = 225.9911 EDISPER = 0.0000
minimization completed, ENE= -.13912717E+05 RMS= 0.180953E+02
minimizing coord set # 4
Total surface charge -13.8196
Reaction field energy -8502.5127
Cavity solvation energy 227.7497
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3894E+04 1.8109E+01 1.1745E+02 CZ 2376
BOND = 4608.0363 ANGLE = 6980.4681 DIHED = 9349.6277
VDWAALS = -5609.2315 EEL = -62920.3291 EPB = -8502.6577
1-4 VDW = 3063.6681 1-4 EEL = 38908.8876 RESTRAINT = 0.0000
ECAVITY = 227.7497 EDISPER = 0.0000
minimization completed, ENE= -.13893781E+05 RMS= 0.181090E+02
minimizing coord set # 5
Total surface charge -13.7319
Reaction field energy -8482.7423
Cavity solvation energy 227.3709
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3711E+04 1.8189E+01 1.3710E+02 N 6435
BOND = 4620.5152 ANGLE = 7121.8783 DIHED = 9426.4939
VDWAALS = -5626.6648 EEL = -62733.4422 EPB = -8482.8937
1-4 VDW = 3017.8424 1-4 EEL = 38717.4553 RESTRAINT = 0.0000
ECAVITY = 227.3709 EDISPER = 0.0000
minimization completed, ENE= -.13711445E+05 RMS= 0.181895E+02
minimizing coord set # 6
Total surface charge -13.7998
Reaction field energy -8523.4839
Cavity solvation energy 228.5470
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3922E+04 1.8148E+01 1.4928E+02 CE2 5367
BOND = 4689.9834 ANGLE = 6964.2324 DIHED = 9403.9800
VDWAALS = -5661.0596 EEL = -62838.6875 EPB = -8523.4528
1-4 VDW = 2994.6426 1-4 EEL = 38820.0688 RESTRAINT = 0.0000
ECAVITY = 228.5470 EDISPER = 0.0000
minimization completed, ENE= -.13921746E+05 RMS= 0.181483E+02
minimizing coord set # 7
Total surface charge -13.8070
Reaction field energy -8433.6854
Cavity solvation energy 228.3669
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.4053E+04 1.7889E+01 1.1255E+02 C 4825
BOND = 4566.6247 ANGLE = 6872.5303 DIHED = 9384.8022
VDWAALS = -5528.3537 EEL = -62979.1975 EPB = -8433.5655
1-4 VDW = 3002.7197 1-4 EEL = 38833.4623 RESTRAINT = 0.0000
ECAVITY = 228.3669 EDISPER = 0.0000
minimization completed, ENE= -.14052611E+05 RMS= 0.178890E+02
minimizing coord set # 8
Total surface charge -13.8261
Reaction field energy -8438.4352
Cavity solvation energy 226.4986
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3941E+04 1.8074E+01 1.2484E+02 N 7435
BOND = 4629.9965 ANGLE = 6988.2505 DIHED = 9421.4561
VDWAALS = -5692.5190 EEL = -62887.0041 EPB = -8438.1663
1-4 VDW = 3024.6799 1-4 EEL = 38785.6546 RESTRAINT = 0.0000
ECAVITY = 226.4986 EDISPER = 0.0000
minimization completed, ENE= -.13941153E+05 RMS= 0.180740E+02
minimizing coord set # 9
Total surface charge -13.8727
Reaction field energy -8450.7124
Cavity solvation energy 227.7989
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3806E+04 1.8059E+01 1.2250E+02 C 8166
BOND = 4705.4364 ANGLE = 6985.9603 DIHED = 9498.9699
VDWAALS = -5682.8523 EEL = -62849.2485 EPB = -8450.5069
1-4 VDW = 3015.1467 1-4 EEL = 38743.6816 RESTRAINT = 0.0000
ECAVITY = 227.7989 EDISPER = 0.0000
minimization completed, ENE= -.13805614E+05 RMS= 0.180593E+02
minimizing coord set # 10
Total surface charge -13.8465
Reaction field energy -8562.1631
Cavity solvation energy 227.9802
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3853E+04 1.7950E+01 1.5088E+02 C 4882
BOND = 4575.0037 ANGLE = 7084.8364 DIHED = 9462.8057
VDWAALS = -5636.2770 EEL = -62770.3518 EPB = -8561.8558
1-4 VDW = 3021.2388 1-4 EEL = 38743.6890 RESTRAINT = 0.0000
ECAVITY = 227.9802 EDISPER = 0.0000
minimization completed, ENE= -.13852931E+05 RMS= 0.179503E+02
minimizing coord set # 11
Total surface charge -13.8116
Reaction field energy -8496.7184
Cavity solvation energy 228.9944
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3972E+04 1.7944E+01 1.1678E+02 CZ2 1600
BOND = 4610.4549 ANGLE = 6940.3163 DIHED = 9320.7975
VDWAALS = -5612.2353 EEL = -62817.0326 EPB = -8496.5925
1-4 VDW = 3007.5750 1-4 EEL = 38845.4210 RESTRAINT = 0.0000
ECAVITY = 228.9944 EDISPER = 0.0000
minimization completed, ENE= -.13972301E+05 RMS= 0.179443E+02
minimizing coord set # 12
Total surface charge -13.7880
Reaction field energy -8482.0065
Cavity solvation energy 227.7961
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3899E+04 1.8129E+01 1.2331E+02 C 2275
BOND = 4597.5470 ANGLE = 7033.1586 DIHED = 9351.9331
VDWAALS = -5706.9962 EEL = -62850.1771 EPB = -8482.0782
1-4 VDW = 3011.9975 1-4 EEL = 38917.9884 RESTRAINT = 0.0000
ECAVITY = 227.7961 EDISPER = 0.0000
minimization completed, ENE= -.13898831E+05 RMS= 0.181286E+02
minimizing coord set # 13
Total surface charge -13.8676
Reaction field energy -8423.6583
Cavity solvation energy 227.3804
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.4028E+04 1.8131E+01 1.2342E+02 C 698
BOND = 4658.3568 ANGLE = 6914.4641 DIHED = 9372.4732
VDWAALS = -5619.5709 EEL = -63061.3054 EPB = -8423.5019
1-4 VDW = 3015.3520 1-4 EEL = 38887.8743 RESTRAINT = 0.0000
ECAVITY = 227.3804 EDISPER = 0.0000
minimization completed, ENE= -.14028478E+05 RMS= 0.181308E+02
minimizing coord set # 14
Total surface charge -13.8221
Reaction field energy -8538.0723
Cavity solvation energy 226.4799
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3880E+04 1.7966E+01 1.2139E+02 CA 3521
BOND = 4557.6328 ANGLE = 7085.0341 DIHED = 9399.7416
VDWAALS = -5653.0389 EEL = -62768.5502 EPB = -8538.1118
1-4 VDW = 2990.5872 1-4 EEL = 38819.8214 RESTRAINT = 0.0000
ECAVITY = 226.4799 EDISPER = 0.0000
minimization completed, ENE= -.13880404E+05 RMS= 0.179663E+02
minimizing coord set # 15
Total surface charge -13.8071
Reaction field energy -8417.6709
Cavity solvation energy 227.9137
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3841E+04 1.8081E+01 1.3804E+02 CZ 11220
BOND = 4682.3971 ANGLE = 7021.0003 DIHED = 9396.1282
VDWAALS = -5675.8102 EEL = -62878.9476 EPB = -8417.8623
1-4 VDW = 3001.7990 1-4 EEL = 38801.9550 RESTRAINT = 0.0000
ECAVITY = 227.9137 EDISPER = 0.0000
minimization completed, ENE= -.13841427E+05 RMS= 0.180813E+02
minimizing coord set # 16
Total surface charge -13.7973
Reaction field energy -8475.5086
Cavity solvation energy 229.4729
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3990E+04 1.7967E+01 1.2593E+02 CZ3 4275
BOND = 4629.5882 ANGLE = 7042.1515 DIHED = 9335.5794
VDWAALS = -5674.1059 EEL = -62853.5614 EPB = -8475.5640
1-4 VDW = 3000.0096 1-4 EEL = 38776.8633 RESTRAINT = 0.0000
ECAVITY = 229.4729 EDISPER = 0.0000
minimization completed, ENE= -.13989566E+05 RMS= 0.179673E+02
minimizing coord set # 17
Total surface charge -13.8459
Reaction field energy -8461.3037
Cavity solvation energy 229.9304
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3994E+04 1.7963E+01 1.1781E+02 CB 3946
BOND = 4663.7088 ANGLE = 6948.0398 DIHED = 9363.2123
VDWAALS = -5638.6882 EEL = -62827.3921 EPB = -8461.2799
1-4 VDW = 3023.9383 1-4 EEL = 38704.1299 RESTRAINT = 0.0000
ECAVITY = 229.9304 EDISPER = 0.0000
minimization completed, ENE= -.13994401E+05 RMS= 0.179634E+02
minimizing coord set # 18
Total surface charge -13.8330
Reaction field energy -8562.7590
Cavity solvation energy 231.6234
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3929E+04 1.8287E+01 1.3387E+02 C 12509
BOND = 4683.8264 ANGLE = 7006.5193 DIHED = 9344.8055
VDWAALS = -5573.3349 EEL = -62809.8472 EPB = -8562.8074
1-4 VDW = 3009.4803 1-4 EEL = 38740.5359 RESTRAINT = 0.0000
ECAVITY = 231.6234 EDISPER = 0.0000
minimization completed, ENE= -.13929199E+05 RMS= 0.182874E+02
minimizing coord set # 19
Total surface charge -13.8423
Reaction field energy -8528.4896
Cavity solvation energy 228.3253
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3888E+04 1.8322E+01 1.3590E+02 C 6036
BOND = 4682.4648 ANGLE = 7048.3036 DIHED = 9313.4188
VDWAALS = -5599.4257 EEL = -62925.6880 EPB = -8528.2244
1-4 VDW = 3047.3558 1-4 EEL = 38845.4348 RESTRAINT = 0.0000
ECAVITY = 228.3253 EDISPER = 0.0000
minimization completed, ENE= -.13888035E+05 RMS= 0.183215E+02
minimizing coord set # 20
Total surface charge -13.8184
Reaction field energy -8585.2157
Cavity solvation energy 227.8094
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.4006E+04 1.7955E+01 1.0946E+02 C 12647
BOND = 4652.9722 ANGLE = 7038.1035 DIHED = 9393.3800
VDWAALS = -5768.6041 EEL = -62618.7117 EPB = -8584.9163
1-4 VDW = 2966.5105 1-4 EEL = 38687.5767 RESTRAINT = 0.0000
ECAVITY = 227.8094 EDISPER = 0.0000
minimization completed, ENE= -.14005880E+05 RMS= 0.179547E+02
minimizing coord set # 21
Total surface charge -13.7554
Reaction field energy -8651.1120
Cavity solvation energy 229.8942
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3785E+04 1.8006E+01 1.3146E+02 CA 4002
BOND = 4663.0646 ANGLE = 7133.6598 DIHED = 9445.3691
VDWAALS = -5669.3831 EEL = -62654.6444 EPB = -8650.9811
1-4 VDW = 2994.9222 1-4 EEL = 38722.6902 RESTRAINT = 0.0000
ECAVITY = 229.8942 EDISPER = 0.0000
minimization completed, ENE= -.13785409E+05 RMS= 0.180059E+02
minimizing coord set # 22
Total surface charge -13.8320
Reaction field energy -8621.1385
Cavity solvation energy 230.2287
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3901E+04 1.7926E+01 1.2380E+02 CZ 3832
BOND = 4675.2325 ANGLE = 6959.0792 DIHED = 9342.9394
VDWAALS = -5660.3801 EEL = -62511.0827 EPB = -8620.9968
1-4 VDW = 3031.9271 1-4 EEL = 38652.2978 RESTRAINT = 0.0000
ECAVITY = 230.2287 EDISPER = 0.0000
minimization completed, ENE= -.13900755E+05 RMS= 0.179263E+02
minimizing coord set # 23
Total surface charge -13.8464
Reaction field energy -8667.1405
Cavity solvation energy 230.4332
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.4000E+04 1.7925E+01 1.2799E+02 CA 3554
BOND = 4598.4715 ANGLE = 6945.7672 DIHED = 9338.2838
VDWAALS = -5555.8402 EEL = -62654.9740 EPB = -8667.1348
1-4 VDW = 3035.5856 1-4 EEL = 38729.8669 RESTRAINT = 0.0000
ECAVITY = 230.4332 EDISPER = 0.0000
minimization completed, ENE= -.13999541E+05 RMS= 0.179249E+02
minimizing coord set # 24
Total surface charge -13.8369
Reaction field energy -8667.1756
Cavity solvation energy 228.9489
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.4002E+04 1.8027E+01 1.1690E+02 C 9108
BOND = 4711.4096 ANGLE = 7062.9502 DIHED = 9296.4014
VDWAALS = -5607.9249 EEL = -62522.0309 EPB = -8667.0078
1-4 VDW = 2927.4118 1-4 EEL = 38567.9514 RESTRAINT = 0.0000
ECAVITY = 228.9489 EDISPER = 0.0000
minimization completed, ENE= -.14001890E+05 RMS= 0.180266E+02
minimizing coord set # 25
Total surface charge -13.7947
Reaction field energy -8588.7816
Cavity solvation energy 229.1442
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3913E+04 1.7981E+01 1.2021E+02 CG 13181
BOND = 4636.1706 ANGLE = 7012.6578 DIHED = 9423.5359
VDWAALS = -5527.6390 EEL = -62762.1330 EPB = -8588.9660
1-4 VDW = 3000.0213 1-4 EEL = 38664.5550 RESTRAINT = 0.0000
ECAVITY = 229.1442 EDISPER = 0.0000
minimization completed, ENE= -.13912653E+05 RMS= 0.179812E+02
minimizing coord set # 26
Total surface charge -13.8108
Reaction field energy -8734.9104
Cavity solvation energy 230.7242
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3900E+04 1.8129E+01 1.4456E+02 C 10792
BOND = 4621.6232 ANGLE = 6916.1504 DIHED = 9448.5807
VDWAALS = -5606.2601 EEL = -62702.2313 EPB = -8735.0258
1-4 VDW = 3026.1364 1-4 EEL = 38900.7465 RESTRAINT = 0.0000
ECAVITY = 230.7242 EDISPER = 0.0000
minimization completed, ENE= -.13899556E+05 RMS= 0.181293E+02
minimizing coord set # 27
Total surface charge -13.9172
Reaction field energy -8782.1519
Cavity solvation energy 231.0171
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.4106E+04 1.7829E+01 1.3623E+02 CD 12150
BOND = 4534.8807 ANGLE = 7002.8750 DIHED = 9332.4057
VDWAALS = -5578.6853 EEL = -62598.8888 EPB = -8781.6776
1-4 VDW = 2992.9606 1-4 EEL = 38759.4701 RESTRAINT = 0.0000
ECAVITY = 231.0171 EDISPER = 0.0000
minimization completed, ENE= -.14105643E+05 RMS= 0.178291E+02
minimizing coord set # 28
Total surface charge -13.8134
Reaction field energy -8694.5170
Cavity solvation energy 231.5840
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3856E+04 1.7992E+01 1.1719E+02 CA 444
BOND = 4674.4595 ANGLE = 7043.0292 DIHED = 9371.9255
VDWAALS = -5547.9128 EEL = -62733.0308 EPB = -8694.8503
1-4 VDW = 2967.1238 1-4 EEL = 38831.7173 RESTRAINT = 0.0000
ECAVITY = 231.5840 EDISPER = 0.0000
minimization completed, ENE= -.13855955E+05 RMS= 0.179921E+02
minimizing coord set # 29
Total surface charge -13.7911
Reaction field energy -8744.4387
Cavity solvation energy 231.8350
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3958E+04 1.8193E+01 1.2300E+02 C 4280
BOND = 4611.3195 ANGLE = 6986.8861 DIHED = 9353.1256
VDWAALS = -5555.0384 EEL = -62626.6953 EPB = -8744.5530
1-4 VDW = 3015.7713 1-4 EEL = 38769.4883 RESTRAINT = 0.0000
ECAVITY = 231.8350 EDISPER = 0.0000
minimization completed, ENE= -.13957861E+05 RMS= 0.181934E+02
minimizing coord set # 30
Total surface charge -13.8246
Reaction field energy -8771.9043
Cavity solvation energy 229.9046
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3975E+04 1.7997E+01 1.1839E+02 C 6119
BOND = 4628.5111 ANGLE = 6950.4406 DIHED = 9402.4819
VDWAALS = -5647.0982 EEL = -62642.8904 EPB = -8771.8367
1-4 VDW = 2995.3146 1-4 EEL = 38880.2812 RESTRAINT = 0.0000
ECAVITY = 229.9046 EDISPER = 0.0000
minimization completed, ENE= -.13974891E+05 RMS= 0.179972E+02
minimizing coord set # 31
Total surface charge -13.8489
Reaction field energy -8825.5522
Cavity solvation energy 233.1773
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3966E+04 1.7882E+01 1.1927E+02 C 9124
BOND = 4634.1710 ANGLE = 6968.5479 DIHED = 9330.4271
VDWAALS = -5527.6426 EEL = -62636.9054 EPB = -8825.5541
1-4 VDW = 3000.6246 1-4 EEL = 38857.5705 RESTRAINT = 0.0000
ECAVITY = 233.1773 EDISPER = 0.0000
minimization completed, ENE= -.13965584E+05 RMS= 0.178818E+02
minimizing coord set # 32
Total surface charge -13.8538
Reaction field energy -8788.0500
Cavity solvation energy 231.3027
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3993E+04 1.8047E+01 1.1755E+02 C 11487
BOND = 4621.0718 ANGLE = 6931.8395 DIHED = 9402.6113
VDWAALS = -5559.7844 EEL = -62695.3641 EPB = -8788.1448
1-4 VDW = 2975.6911 1-4 EEL = 38887.3960 RESTRAINT = 0.0000
ECAVITY = 231.3027 EDISPER = 0.0000
minimization completed, ENE= -.13993381E+05 RMS= 0.180468E+02
minimizing coord set # 33
Total surface charge -13.8449
Reaction field energy -8801.7799
Cavity solvation energy 229.7037
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3999E+04 1.7970E+01 1.2416E+02 C 8931
BOND = 4624.8747 ANGLE = 6969.8678 DIHED = 9400.1928
VDWAALS = -5669.9125 EEL = -62666.4526 EPB = -8801.7593
1-4 VDW = 3001.6168 1-4 EEL = 38912.4610 RESTRAINT = 0.0000
ECAVITY = 229.7037 EDISPER = 0.0000
minimization completed, ENE= -.13999408E+05 RMS= 0.179698E+02
minimizing coord set # 34
Total surface charge -13.8233
Reaction field energy -8764.9277
Cavity solvation energy 231.2189
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3842E+04 1.7883E+01 1.2338E+02 C 8782
BOND = 4661.6798 ANGLE = 6965.9293 DIHED = 9427.8902
VDWAALS = -5618.7411 EEL = -62609.3112 EPB = -8765.3093
1-4 VDW = 3026.7777 1-4 EEL = 38837.6420 RESTRAINT = 0.0000
ECAVITY = 231.2189 EDISPER = 0.0000
minimization completed, ENE= -.13842224E+05 RMS= 0.178834E+02
minimizing coord set # 35
Total surface charge -13.8733
Reaction field energy -8700.1478
Cavity solvation energy 230.0558
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3874E+04 1.8210E+01 1.2631E+02 CA 9803
BOND = 4680.4973 ANGLE = 7077.2777 DIHED = 9342.9448
VDWAALS = -5660.9564 EEL = -62791.7740 EPB = -8700.0624
1-4 VDW = 3035.1053 1-4 EEL = 38913.1334 RESTRAINT = 0.0000
ECAVITY = 230.0558 EDISPER = 0.0000
minimization completed, ENE= -.13873779E+05 RMS= 0.182101E+02
minimizing coord set # 36
Total surface charge -13.8326
Reaction field energy -8684.3403
Cavity solvation energy 230.0981
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3979E+04 1.8025E+01 1.1644E+02 C 3416
BOND = 4642.7007 ANGLE = 6947.9079 DIHED = 9360.8231
VDWAALS = -5604.4802 EEL = -62829.7450 EPB = -8684.6043
1-4 VDW = 2994.4910 1-4 EEL = 38963.7073 RESTRAINT = 0.0000
ECAVITY = 230.0981 EDISPER = 0.0000
minimization completed, ENE= -.13979101E+05 RMS= 0.180253E+02
minimizing coord set # 37
Total surface charge -13.7960
Reaction field energy -8635.1031
Cavity solvation energy 229.5170
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3778E+04 1.8221E+01 1.3135E+02 C 382
BOND = 4785.9408 ANGLE = 6985.2320 DIHED = 9461.7279
VDWAALS = -5678.2077 EEL = -62655.6098 EPB = -8635.1570
1-4 VDW = 2967.9520 1-4 EEL = 38760.9054 RESTRAINT = 0.0000
ECAVITY = 229.5170 EDISPER = 0.0000
minimization completed, ENE= -.13777699E+05 RMS= 0.182213E+02
minimizing coord set # 38
Total surface charge -13.8354
Reaction field energy -8639.5432
Cavity solvation energy 230.0825
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3761E+04 1.8069E+01 1.4042E+02 C 5055
BOND = 4608.2940 ANGLE = 6997.9301 DIHED = 9407.4099
VDWAALS = -5601.6543 EEL = -62733.4726 EPB = -8639.7807
1-4 VDW = 3074.0797 1-4 EEL = 38896.4339 RESTRAINT = 0.0000
ECAVITY = 230.0825 EDISPER = 0.0000
minimization completed, ENE= -.13760677E+05 RMS= 0.180686E+02
minimizing coord set # 39
Total surface charge -13.8310
Reaction field energy -8603.6636
Cavity solvation energy 228.2460
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3924E+04 1.8076E+01 1.2301E+02 CA 5890
BOND = 4666.2253 ANGLE = 6957.0715 DIHED = 9343.7017
VDWAALS = -5650.6790 EEL = -62847.2256 EPB = -8603.6787
1-4 VDW = 3024.9121 1-4 EEL = 38956.9366 RESTRAINT = 0.0000
ECAVITY = 228.2460 EDISPER = 0.0000
minimization completed, ENE= -.13924490E+05 RMS= 0.180758E+02
minimizing coord set # 40
Total surface charge -13.8097
Reaction field energy -8589.6509
Cavity solvation energy 230.0260
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3833E+04 1.8128E+01 1.4927E+02 C 2328
BOND = 4588.9622 ANGLE = 7058.5503 DIHED = 9395.4630
VDWAALS = -5619.5915 EEL = -62774.9967 EPB = -8589.5225
1-4 VDW = 2997.1698 1-4 EEL = 38881.2587 RESTRAINT = 0.0000
ECAVITY = 230.0260 EDISPER = 0.0000
minimization completed, ENE= -.13832681E+05 RMS= 0.181281E+02
minimizing coord set # 41
Total surface charge -13.7940
Reaction field energy -8743.3999
Cavity solvation energy 229.6476
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3902E+04 1.8160E+01 1.4161E+02 C 8262
BOND = 4680.8614 ANGLE = 6915.8287 DIHED = 9365.4825
VDWAALS = -5628.7360 EEL = -62467.6537 EPB = -8743.4992
1-4 VDW = 3002.4430 1-4 EEL = 38744.0182 RESTRAINT = 0.0000
ECAVITY = 229.6476 EDISPER = 0.0000
minimization completed, ENE= -.13901607E+05 RMS= 0.181601E+02
minimizing coord set # 42
Total surface charge -13.7442
Reaction field energy -8583.0493
Cavity solvation energy 229.5365
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3906E+04 1.8103E+01 1.2576E+02 C 2604
BOND = 4680.4619 ANGLE = 7010.6557 DIHED = 9386.7691
VDWAALS = -5697.4674 EEL = -62794.6561 EPB = -8583.2882
1-4 VDW = 3011.7927 1-4 EEL = 38849.9223 RESTRAINT = 0.0000
ECAVITY = 229.5365 EDISPER = 0.0000
minimization completed, ENE= -.13906274E+05 RMS= 0.181030E+02
minimizing coord set # 43
Total surface charge -13.8105
Reaction field energy -8570.9811
Cavity solvation energy 229.9407
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3873E+04 1.8121E+01 1.2744E+02 CG 842
BOND = 4677.7687 ANGLE = 7034.2461 DIHED = 9355.7298
VDWAALS = -5617.0338 EEL = -62792.5415 EPB = -8571.0228
1-4 VDW = 2994.6708 1-4 EEL = 38815.4069 RESTRAINT = 0.0000
ECAVITY = 229.9407 EDISPER = 0.0000
minimization completed, ENE= -.13872835E+05 RMS= 0.181208E+02
minimizing coord set # 44
Total surface charge -13.7955
Reaction field energy -8603.2320
Cavity solvation energy 229.2974
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3909E+04 1.8184E+01 1.1689E+02 C 8225
BOND = 4679.8251 ANGLE = 6983.5623 DIHED = 9382.9872
VDWAALS = -5647.2374 EEL = -62725.1059 EPB = -8603.3655
1-4 VDW = 2996.0028 1-4 EEL = 38794.5893 RESTRAINT = 0.0000
ECAVITY = 229.2974 EDISPER = 0.0000
minimization completed, ENE= -.13909445E+05 RMS= 0.181844E+02
minimizing coord set # 45
Total surface charge -13.8841
Reaction field energy -8611.4564
Cavity solvation energy 227.6548
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3865E+04 1.8178E+01 1.2318E+02 C 1301
BOND = 4709.2016 ANGLE = 6992.9976 DIHED = 9340.1849
VDWAALS = -5624.7098 EEL = -62698.3120 EPB = -8611.4242
1-4 VDW = 3003.6219 1-4 EEL = 38795.6120 RESTRAINT = 0.0000
ECAVITY = 227.6548 EDISPER = 0.0000
minimization completed, ENE= -.13865173E+05 RMS= 0.181785E+02
minimizing coord set # 46
Total surface charge -13.8428
Reaction field energy -8532.8491
Cavity solvation energy 228.4813
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3901E+04 1.8161E+01 1.3988E+02 C 2464
BOND = 4680.8006 ANGLE = 6926.2228 DIHED = 9394.3454
VDWAALS = -5637.2067 EEL = -62817.4083 EPB = -8532.8554
1-4 VDW = 3029.0495 1-4 EEL = 38827.2419 RESTRAINT = 0.0000
ECAVITY = 228.4813 EDISPER = 0.0000
minimization completed, ENE= -.13901329E+05 RMS= 0.181607E+02
minimizing coord set # 47
Total surface charge -13.8759
Reaction field energy -8610.3317
Cavity solvation energy 229.3316
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3852E+04 1.7971E+01 1.1940E+02 C 10537
BOND = 4612.3390 ANGLE = 7080.5574 DIHED = 9347.0127
VDWAALS = -5543.6296 EEL = -62900.9176 EPB = -8610.0300
1-4 VDW = 2983.1943 1-4 EEL = 38950.5065 RESTRAINT = 0.0000
ECAVITY = 229.3316 EDISPER = 0.0000
minimization completed, ENE= -.13851636E+05 RMS= 0.179714E+02
minimizing coord set # 48
Total surface charge -13.8592
Reaction field energy -8598.7820
Cavity solvation energy 228.3408
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3963E+04 1.8131E+01 1.2562E+02 CD2 1678
BOND = 4677.9836 ANGLE = 6995.5801 DIHED = 9382.3697
VDWAALS = -5652.8238 EEL = -62786.2180 EPB = -8598.8187
1-4 VDW = 3000.4017 1-4 EEL = 38789.7079 RESTRAINT = 0.0000
ECAVITY = 228.3408 EDISPER = 0.0000
minimization completed, ENE= -.13963477E+05 RMS= 0.181310E+02
minimizing coord set # 49
Total surface charge -13.8328
Reaction field energy -8538.5907
Cavity solvation energy 228.4389
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.4111E+04 1.7956E+01 1.1314E+02 C 13294
BOND = 4669.1511 ANGLE = 6918.6457 DIHED = 9334.8467
VDWAALS = -5655.6540 EEL = -62895.5312 EPB = -8538.8531
1-4 VDW = 2962.4438 1-4 EEL = 38865.4145 RESTRAINT = 0.0000
ECAVITY = 228.4389 EDISPER = 0.0000
minimization completed, ENE= -.14111097E+05 RMS= 0.179562E+02
minimizing coord set # 50
Total surface charge -13.8028
Reaction field energy -8574.0462
Cavity solvation energy 226.7747
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.3979E+04 1.7881E+01 1.2747E+02 C 6352
BOND = 4616.5859 ANGLE = 6997.7140 DIHED = 9349.2971
VDWAALS = -5600.6459 EEL = -62811.8254 EPB = -8573.7923
1-4 VDW = 2980.9506 1-4 EEL = 38835.7241 RESTRAINT = 0.0000
ECAVITY = 226.7747 EDISPER = 0.0000
minimization completed, ENE= -.13979217E+05 RMS= 0.178806E+02
TRAJENE: Trajectory file ended
TRAJENE: Trajene complete.
--------------------------------------------------------------------------------
5. TIMINGS
--------------------------------------------------------------------------------
| PB Nonbond 15585.76 (100.0% of Nonbo)
| Nonbond force 15585.81 (100.0% of Force)
| Bond/Angle/Dihedral 5.40 ( 0.03% of Force)
| Force time 15591.41 (100.0% of Runmd)
| Runmd Time 15591.41 (99.90% of Total)
| Other 15.73 ( 0.10% of Total)
| Total time 15607.19 (100.0% of ALL )
| Highest rstack allocated: 0
| Highest istack allocated: 0
| Job began at 19:15:19.532 on 05/19/2011
| Setup done at 19:15:19.963 on 05/19/2011
| Run done at 23:35:26.726 on 05/19/2011
| wallclock() was called 1209 times
The format of _MMPBSA_ligand_pb.mdout is similar with the
_MMPBSA_receptor_pb.mdout, but with different values. Could you let me know
what information I should get from these files? Thank you very much!
________________________________
From: Bill Miller III <brmilleriii.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Fri, May 20, 2011 3:41:36 PM
Subject: Re: [AMBER] Problem of PB calculation when running mmpbsa.py
What did your MMPBSA.py input file look like? Also, there should have been
some _MMPBSA_*_pb.mdout files created for the complex, receptor, and
protein. My guess is there are some helpful information/messages in those
files.
-Bill
On Fri, May 20, 2011 at 3:36 PM, bin wang <wang_p_z.yahoo.com.cn> wrote:
> Hello Amber users,
> When I use mmpbsa.py to calculate binding energy of a protein-protein
> interaction, the result.dat file only showed the GB part but not the PB
> part.
> The messages are listed as follows:
>
> ptraj found! Using /opt/amber11/bin/ptraj
> sander found! Using /opt/amber11/bin/sander (serial only!)
>
> Preparing trajectories with ptraj...
> 50 frames were read in and processed by ptraj for use in calculation.
>
> Starting sander calls
>
> Starting gb calculation...
>
> Starting pb calculation...
>
> Error: No potential terms in sander output! Check output files.
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
>
> When I caculated a protein-DNA interaction, the result showed both PB and
> GB,
> but for this one, it only showed GB. I don't know what could possibly
> cause
> this problem. Need your help. Thank you.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri May 20 2011 - 13:30:04 PDT
