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

| Run on 12/30/2013 at 09:10:59
  [-O]verwriting output

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

|INPTRA: _MMPBSA_receptor.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 = 09:43:31
 NATOM  =     870 NTYPES =      39 NBONH =     304 MBONA  =     638
 NTHETH =     719 MTHETA =     987 NPHIH =    1200 MPHIA  =    1850
 NHPARM =       0 NPARM  =       0 NNB   =    4862 NRES   =      27
 NBONA  =     638 NTHETA =     987 NPHIA =    1850 NUMBND =      60
 NUMANG =     120 NPTRA  =     231 NATYP =      39 NPHB   =       0
 IFBOX  =       0 NMXRS  =      33 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               62081
|     Hollerith           2639
|     Integer            66788
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              756 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      25.6751
 Reaction field energy  -8184.6397
 Cavity solvation energy    558.5023
 Dispersion solvation energy   -558.9760
| PB NB list                     0.04
| PB FD grid                     0.02
| PB Sasa                        0.92
| PB FD force                    2.73
| PB Set linear sys              0.75
| PB Solver                      1.53
| PB Direct                      0.02
| NP Sasa                        0.04
| NP Cavity                      0.00
| NP Dispersion                  1.54
| PB SA srf                      0.05
| PB SA arc                      0.86
| PB SA arc setup                0.01
| PB circle                      0.76
| PB exclude                     0.09
| PB exmol                       0.72
| PB exmol setup                 0.12
| PB exmol part a                0.02
| PB exmol part b                0.07
| PB exmol part c                0.02
| PB exmol part d                0.01
| PB exmol part e                0.17
| 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                        0.92
| PB FD force                    1.61
| PB Set linear sys              0.63
| PB Solver                      0.53
| PB Multiple                    0.00
| PB Direct                      0.02
| NP Sasa                        0.04
| NP Cavity                      0.00
| NP Dispersion                  1.46
| PB SA srf                      0.05
| PB SA arc                      0.87
| PB SA arc setup                0.01
| PB circle                      0.79
| PB exclude                     0.07
| PB exmol                       0.62
| PB exmol setup                 0.08
| PB exmol part a                0.00
| PB exmol part b                0.06
| PB exmol part c                0.02
| PB exmol part d                0.01
| PB exmol part e                0.17
| PB exmol part f                0.16
| PB epsbnd                      0.00
| PB epsmap                      0.03
| PB calsa                       0.00


                    FINAL RESULTS



   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1       7.2813E+05     2.0945E+01     1.0540E+02     C3'       478

 BOND    =      291.8385  ANGLE   =      547.2881  DIHED      =      890.7924
 UB      =   731605.3804  IMP     =      396.5639  CMAP       =        0.0000
 VDWAALS =     -472.0484  EEL     =     5468.2573  EPB        =    -8184.7238
 1-4 VDW =      446.0243  1-4 EEL =    -2860.6778  RESTRAINT  =        0.0000
 ECAVITY =      558.5023  EDISPER =     -558.9760
minimization completed, ENE= 0.72812822E+06 RMS= 0.209452E+02
minimizing coord set #     2
| PB NB list                     0.02
| PB FD grid                     0.03
| PB Sasa                        0.88
| PB FD force                    2.59
| PB Set linear sys              0.74
| PB Solver                      1.40
| PB Multiple                    0.00
| PB Direct                      0.02
| NP Sasa                        0.04
| NP Cavity                      0.00
| NP Dispersion                  1.51
| PB SA srf                      0.05
| PB SA arc                      0.83
| PB SA arc setup                0.01
| PB circle                      0.75
| PB exclude                     0.08
| PB exmol                       0.71
| PB exmol setup                 0.12
| 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                0.18
| PB exmol part f                0.17
| PB epsbnd                      0.01
| PB epsmap                      0.03
| PB calsa                       0.00


  Maximum number of minimization cycles reached.
| PB NB list                     0.00
| PB FD grid                     0.00
| PB Sasa                        0.85
| PB FD force                    1.61
| PB Set linear sys              0.63
| PB Solver                      0.53
| PB Multiple                    0.00
| PB Direct                      0.02
| NP Sasa                        0.04
| NP Cavity                      0.00
| NP Dispersion                  1.47
| PB SA srf                      0.05
| PB SA arc                      0.80
| PB SA arc setup                0.01
| PB circle                      0.73
| PB exclude                     0.07
| PB exmol                       0.62
| PB exmol setup                 0.08
| PB exmol part a                0.00
| PB exmol part b                0.06
| 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                      0.00
| PB epsmap                      0.03
| PB calsa                       0.00


                    FINAL RESULTS



   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1       5.1203E+05     2.0453E+01     1.0060E+02     C1'       225

 BOND    =      278.5144  ANGLE   =      504.6488  DIHED      =      898.9582
 UB      =   515828.3425  IMP     =      127.5608  CMAP       =        0.0000
 VDWAALS =     -462.7621  EEL     =     5361.0385  EPB        =    -8099.3929
 1-4 VDW =      440.4165  1-4 EEL =    -2843.1555  RESTRAINT  =        0.0000
 ECAVITY =      563.4304  EDISPER =     -563.6467
minimization completed, ENE= 0.51203395E+06 RMS= 0.204528E+02
TRAJENE: Trajectory file ended
TRAJENE: Trajene complete.

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

|    Read coords time           0.00 ( 0.01% of Total)
|             PB Nonbond                12.32 (66.70% of Nonbo)
|             NP Nonbond                 6.15 (33.30% of Nonbo)
|          Nonbond force             18.47 (99.89% of Force)
|          Bond/Angle/Dihedral        0.02 ( 0.11% of Force)
|       Force time                18.49 (100.0% of Runmd)
|    Runmd Time                18.49 (99.64% of Total)
|    Other                      0.06 ( 0.35% of Total)
| Total time                18.55 (100.0% of ALL  )

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

| Final Performance Info:
| -----------------------------------------------------
| Average timings for all steps:
|     Elapsed(s) =      18.51 Per Step(ms) =   18506.67
|         ns/day =       0.00   seconds/ns = **********
| -----------------------------------------------------

|           Job began  at 09:10:59.378  on 12/30/2013
|           Setup done at 09:10:59.425  on 12/30/2013
|           Run   done at 09:11:17.932  on 12/30/2013
|     wallclock() was called     403 times
