
          -------------------------------------------------------
          Amber 12 SANDER                              2012
          -------------------------------------------------------

| Run on 12/30/2013 at 09:10:38
  [-O]verwriting output

File Assignments:
|  MDIN: _MMPBSA_pb.mdin                                                       
| MDOUT: _MMPBSA_complex_pb.mdout.0                                            
|INPCRD: _MMPBSA_dummycomplex.inpcrd                                           
|  PARM: DNA_AMP_ante.prmtop                                                   
|RESTRT: _MMPBSA_restrt.0                                                      
|  REFC: refc                                                                  
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: mdcrd                                                                 
|MDINFO: mdinfo                                                                
|  MTMD: mtmd                                                                  
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                

|INPTRA: _MMPBSA_complex.mdcrd.0                                               
|

 Here is the input file:

File generated by MMPBSA.py                                                    
&cntrl                                                                         
 nsnb=99999, dec_verbose=0, ipb=2,                                             
 ntb=0, cut=999.0, imin=5, igb=10,                                             
/                                                                              
&pb                                                                            
 maxitn=1000, fillratio=4.0, radiopt=0,                                        
/                                                                              

--------------------------------------------------------------------------------
   1.  RESOURCE   USE: 
--------------------------------------------------------------------------------

| Flags:                                                                        
| New format PARM file being parsed.
| Version =    1.000 Date = 12/27/13 Time = 09:43:30
 NATOM  =     940 NTYPES =      39 NBONH =     328 MBONA  =     688
 NTHETH =     771 MTHETA =    1063 NPHIH =    1300 MPHIA  =    1966
 NHPARM =       0 NPARM  =       0 NNB   =    5228 NRES   =      29
 NBONA  =     688 NTHETA =    1063 NPHIA =    1966 NUMBND =      65
 NUMANG =     138 NPTRA  =     280 NATYP =      39 NPHB   =       0
 IFBOX  =       0 NMXRS  =      35 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   
| Force field information read from topology file: 
| CHARMM 271       *  \\\\ CHARMM27 All-Hydrogen Nucleic Acid Topology File ///   
|
|CHARMM: CHARMM force field in use. 
|CHARMM: Overriding default value of chngmask.
|CHARMM: Setting chngmask = 0.

|     Memory Use     Allocated
|     Real               66931
|     Hollerith           2851
|     Integer            70186
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              808 kbytes

| Note: 1-4 EEL scale factors are being read from the topology file.

| Note: 1-4 VDW scale factors are being read from the topology file.
| 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    =      50, 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  =       1, ncyc    =      10, ntmin   =       1
     dx0     =   0.01000, drms    =   0.00010
|  INFO: Old style inpcrd file read


--------------------------------------------------------------------------------
   3.  ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

Cpptraj Generated Restart                                                       
 begin time read from input coords =     1.000 ps

 Number of triangulated 3-point waters found:        0

--------------------------------------------------------------------------------
   4.  RESULTS
--------------------------------------------------------------------------------

 POST-PROCESSING OF TRAJECTORY ENERGIES
Cpptraj Generated trajectory                                                    
minimizing coord set #     1
 Total surface charge      29.6278
 Reaction field energy -10770.4521
 Cavity solvation energy    591.8419
 Dispersion solvation energy   -572.7632
| PB NB list                     0.04
| PB FD grid                     0.02
| PB Sasa                        1.09
| PB FD force                    2.92
| PB Set linear sys              0.80
| PB Solver                      1.62
| PB Multiple                    0.00
| PB Direct                      0.03
| NP Sasa                        0.04
| NP Cavity                      0.00
| NP Dispersion                  1.65
| PB SA srf                      0.06
| PB SA arc                      1.04
| PB SA arc setup                0.01
| PB circle                      0.93
| PB exclude                     0.09
| PB exmol                       0.77
| PB exmol setup                 0.14
| PB exmol part a                0.04
| PB exmol part b                0.08
| PB exmol part c                0.02
| PB exmol part d                0.01
| PB exmol part e                0.19
| PB exmol part f                0.16
| PB epsbnd                      0.01
| PB epsmap                      0.04
| PB calsa                       0.00


  Maximum number of minimization cycles reached.
| PB NB list                     0.00
| PB FD grid                     0.00
| PB Sasa                        0.99
| PB FD force                    1.73
| PB Set linear sys              0.66
| PB Solver                      0.58
| PB Multiple                    0.00
| PB Direct                      0.03
| NP Sasa                        0.04
| NP Cavity                      0.00
| NP Dispersion                  1.63
| PB SA srf                      0.06
| PB SA arc                      0.94
| PB SA arc setup                0.01
| PB circle                      0.86
| PB exclude                     0.07
| PB exmol                       0.65
| PB exmol setup                 0.09
| PB exmol part a                0.00
| PB exmol part b                0.07
| PB exmol part c                0.02
| PB exmol part d                0.01
| PB exmol part e                0.18
| PB exmol part f                0.16
| PB epsbnd                      0.01
| PB epsmap                      0.03
| PB calsa                       0.00


                    FINAL RESULTS



   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1      -4.0253E+03     2.0971E+01     1.0541E+02     C3'       478

 BOND    =      322.2021  ANGLE   =      618.5524  DIHED      =      950.5220
 UB      =      200.0067  IMP     =       12.6237  CMAP       =        0.0000
 VDWAALS =     -530.3789  EEL     =     7223.9037  EPB        =   -10770.4176
 1-4 VDW =      478.7669  1-4 EEL =    -2550.1967  RESTRAINT  =        0.0000
 ECAVITY =      591.8419  EDISPER =     -572.7632
minimization completed, ENE= -.40253371E+04 RMS= 0.209709E+02
minimizing coord set #     2
| PB NB list                     0.02
| PB FD grid                     0.03
| PB Sasa                        1.01
| PB FD force                    2.76
| PB Set linear sys              0.79
| PB Solver                      1.47
| PB Multiple                    0.00
| PB Direct                      0.03
| NP Sasa                        0.04
| NP Dispersion                  1.73
| PB SA srf                      0.06
| PB SA arc                      0.95
| PB SA arc setup                0.01
| PB circle                      0.85
| PB exclude                     0.09
| PB exmol                       0.76
| PB exmol setup                 0.13
| PB exmol part a                0.02
| PB exmol part b                0.08
| PB exmol part c                0.02
| PB exmol part d                0.01
| PB exmol part e                0.19
| PB exmol part f                0.17
| PB epsbnd                      0.01
| PB epsmap                      0.04
| PB calsa                       0.00


  Maximum number of minimization cycles reached.
| PB NB list                     0.00
| PB FD grid                     0.00
| PB Sasa                        1.01
| PB FD force                    1.73
| PB Set linear sys              0.66
| PB Solver                      0.57
| PB Multiple                    0.00
| PB Direct                      0.03
| NP Sasa                        0.04
| NP Cavity                      0.00
| NP Dispersion                  1.64
| PB SA srf                      0.06
| PB SA arc                      0.95
| PB SA arc setup                0.01
| PB circle                      0.87
| PB exclude                     0.08
| PB exmol                       0.65
| PB exmol setup                 0.08
| PB exmol part a                0.00
| PB exmol part b                0.07
| PB exmol part c                0.02
| PB exmol part d                0.01
| PB exmol part e                0.18
| PB exmol part f                0.17
| PB epsbnd                      0.00
| PB epsmap                      0.03
| PB calsa                       0.00


                    FINAL RESULTS



   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1      -4.0927E+03     2.0539E+01     1.0090E+02     C1'       225

 BOND    =      301.9724  ANGLE   =      566.7113  DIHED      =      948.0969
 UB      =      208.6236  IMP     =       20.5150  CMAP       =        0.0000
 VDWAALS =     -525.0397  EEL     =     7030.1991  EPB        =   -10609.4126
 1-4 VDW =      478.9557  1-4 EEL =    -2529.6343  RESTRAINT  =        0.0000
 ECAVITY =      598.3765  EDISPER =     -582.0542
minimization completed, ENE= -.40926902E+04 RMS= 0.205389E+02
TRAJENE: Trajectory file ended
TRAJENE: Trajene complete.

--------------------------------------------------------------------------------
   5.  TIMINGS
--------------------------------------------------------------------------------

|    Read coords time           0.00 ( 0.01% of Total)
|             PB Nonbond                13.48 (66.38% of Nonbo)
|             NP Nonbond                 6.83 (33.62% of Nonbo)
|          Nonbond force             20.31 (99.89% of Force)
|          Bond/Angle/Dihedral        0.02 ( 0.11% of Force)
|       Force time                20.33 (100.0% of Runmd)
|    Runmd Time                20.33 (99.63% of Total)
|    Other                      0.07 ( 0.36% of Total)
| Total time                20.41 (100.0% of ALL  )

| Highest rstack allocated:          0
| Highest istack allocated:          0

| Final Performance Info:
| -----------------------------------------------------
| Average timings for all steps:
|     Elapsed(s) =      20.35 Per Step(ms) =   20352.43
|         ns/day =       0.00   seconds/ns = **********
| -----------------------------------------------------

|           Job began  at 09:10:38.938  on 12/30/2013
|           Setup done at 09:10:38.992  on 12/30/2013
|           Run   done at 09:10:59.345  on 12/30/2013
|     wallclock() was called     403 times
