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

| Run on 12/30/2013 at 09:11:17
  [-O]verwriting output

File Assignments:
|  MDIN: _MMPBSA_pb.mdin                                                       
| MDOUT: _MMPBSA_ligand_pb.mdout.0                                             
|INPCRD: _MMPBSA_dummyligand.inpcrd                                            
|  PARM: 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_ligand.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 = 09:43:32
 NATOM  =      70 NTYPES =      39 NBONH =      24 MBONA  =      50
 NTHETH =      52 MTHETA =      76 NPHIH =     100 MPHIA  =     116
 NHPARM =       0 NPARM  =       0 NNB   =     366 NRES   =       2
 NBONA  =      50 NTHETA =      76 NPHIA =     116 NUMBND =      28
 NUMANG =      54 NPTRA  =     100 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                6541
|     Hollerith            214
|     Integer            24924
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              149 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       3.9500
 Reaction field energy   -669.1295
 Cavity solvation energy     63.2419
 Dispersion solvation energy    -76.3404
| PB NB list                     0.00
| PB FD grid                     0.01
| PB Sasa                        0.04
| PB FD force                    0.29
| PB Set linear sys              0.10
| PB Solver                      0.18
| PB Direct                      0.00
| NP Sasa                        0.00
| NP Cavity                      0.00
| NP Dispersion                  0.02
| PB SA srf                      0.01
| PB SA arc                      0.04
| PB SA arc setup                0.00
| PB circle                      0.03
| PB exclude                     0.00
| PB exmol                       0.10
| PB exmol setup                 0.03
| PB exmol part a                0.00
| PB exmol part b                0.01
| PB exmol part c                0.00
| PB exmol part d                0.00
| PB exmol part e                0.01
| PB exmol part f                0.02
| PB epsbnd                      0.00
| PB epsmap                      0.01
| PB calsa                       0.00


  Maximum number of minimization cycles reached.
| PB NB list                     0.00
| PB FD grid                     0.00
| PB Sasa                        0.04
| PB FD force                    0.15
| PB Set linear sys              0.08
| PB Solver                      0.07
| PB Direct                      0.00
| NP Sasa                        0.00
| NP Dispersion                  0.02
| PB SA srf                      0.00
| PB SA arc                      0.03
| PB SA arc setup                0.00
| PB circle                      0.03
| PB exclude                     0.00
| PB exmol                       0.08
| PB exmol setup                 0.02
| PB exmol part a                0.00
| PB exmol part b                0.01
| PB exmol part c                0.00
| PB exmol part d                0.00
| PB exmol part e                0.01
| PB exmol part f                0.02
| PB epsbnd                      0.00
| PB epsmap                      0.01
| PB calsa                       0.00


                    FINAL RESULTS



   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1              NaN     1.9793E+03     2.5136E+04     O3'        61

 BOND    =       30.3636  ANGLE   =       71.2643  DIHED      =       59.7296
 UB      =           NaN  IMP     =    27503.4708  CMAP       =        0.0000
 VDWAALS =       -3.0069  EEL     =     -220.7480  EPB        =     -669.1427
 1-4 VDW =       32.7426  1-4 EEL =      310.4811  RESTRAINT  =        0.0000
 ECAVITY =       63.2419  EDISPER =      -76.3404
minimization completed, ENE=            NaN RMS= 0.197926E+04
minimizing coord set #     2
| PB NB list                     0.00
| PB FD grid                     0.01
| PB Sasa                        0.04
| PB FD force                    0.31
| PB Set linear sys              0.10
| PB Solver                      0.20
| PB Multiple                    0.00
| PB Direct                      0.00
| NP Sasa                        0.00
| NP Cavity                      0.00
| NP Dispersion                  0.02
| PB SA srf                      0.00
| PB SA arc                      0.03
| PB SA arc setup                0.00
| PB circle                      0.03
| PB exclude                     0.00
| PB exmol                       0.10
| PB exmol setup                 0.03
| PB exmol part a                0.00
| PB exmol part b                0.01
| PB exmol part c                0.00
| PB exmol part d                0.00
| PB exmol part e                0.01
| PB exmol part f                0.02
| PB epsbnd                      0.00
| PB epsmap                      0.01
| PB calsa                       0.00


  Maximum number of minimization cycles reached.
| PB NB list                     0.00
| PB FD grid                     0.00
| PB Sasa                        0.07
| PB FD force                    0.16
| PB Set linear sys              0.08
| PB Solver                      0.07
| PB Multiple                    0.00
| PB Direct                      0.00
| NP Sasa                        0.00
| NP Cavity                      0.00
| NP Dispersion                  0.02
| PB SA srf                      0.00
| PB SA arc                      0.06
| PB SA arc setup                0.00
| PB circle                      0.04
| PB exclude                     0.02
| PB exmol                       0.08
| PB exmol setup                 0.02
| PB exmol part a                0.00
| PB exmol part b                0.01
| PB exmol part c                0.00
| PB exmol part d                0.00
| PB exmol part e                0.01
| PB exmol part f                0.02
| PB epsbnd                      0.00
| PB epsmap                      0.01
| PB calsa                       0.00


                    FINAL RESULTS



   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
      1              NaN     1.8101E+03     2.1402E+04     O3'        61

 BOND    =       23.4581  ANGLE   =       62.0625  DIHED      =       49.1386
 UB      =           NaN  IMP     =    25910.6092  CMAP       =        0.0000
 VDWAALS =      -12.2127  EEL     =     -161.9127  EPB        =     -715.8410
 1-4 VDW =       38.5392  1-4 EEL =      313.5212  RESTRAINT  =        0.0000
 ECAVITY =       64.4799  EDISPER =      -78.8298
minimization completed, ENE=            NaN RMS= 0.181008E+04
TRAJENE: Trajectory file ended
TRAJENE: Trajene complete.

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

|    Read coords time           0.00 ( 0.05% of Total)
|             PB Nonbond                 1.11 (93.27% of Nonbo)
|             NP Nonbond                 0.08 ( 6.73% of Nonbo)
|          Nonbond force              1.19 (99.44% of Force)
|          Bond/Angle/Dihedral        0.01 ( 0.55% of Force)
|          Other                      0.00 ( 0.01% of Force)
|       Force time                 1.20 (100.0% of Runmd)
|    Runmd Time                 1.20 (98.45% of Total)
|    Other                      0.02 ( 1.49% of Total)
| Total time                 1.21 (100.0% of ALL  )

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

| Final Performance Info:
| -----------------------------------------------------
| Average timings for all steps:
|     Elapsed(s) =       1.20 Per Step(ms) =    1198.46
|         ns/day =       0.07   seconds/ns = 1198458.97
| -----------------------------------------------------

|           Job began  at 09:11:17.963  on 12/30/2013
|           Setup done at 09:11:17.980  on 12/30/2013
|           Run   done at 09:11:19.178  on 12/30/2013
|     wallclock() was called     403 times
