
 OPTIM version 22983, Copyright (C) David J. Wales
 OPTIM comes with ABSOLUTELY NO WARRANTY; for details supply WARRANTY as an input keyword.
 This is free software, and you are welcome to redistribute it
 under certain conditions; provide keyword COPYRIGHT to see the details.

 getparams> input coordinates for AMBER9 system will be read from 
start
start               

          -------------------------------------------------------
          Amber 9  SANDER                              2006
          -------------------------------------------------------

| Run on 05/23/2012 at 21:01:55
  [-O]verwriting output

File Assignments:
|  MDIN: min.in                                                                
| MDOUT: min.out                                                               
|INPCRD: coords.inpcrd                                                         
|  PARM: coords.prmtop                                                         
|RESTRT: coords.rst                                                            
|  REFC: refc                                                                  
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: coords.mdcrd                                                          
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                


 Here is the input file:

Minimization                                                                   
&cntrl                                                                         
   imin=1, maxcyc=1, ncyc=1,                                                   
   igb=2, saltcon=0.2,                                                         
   ntpr=1, ntx=1, ntb=0,                                                       
   cut = 999.0                                                                 
 /                                                                             
	                                                                              

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

| Flags:                                                                        
| New format PARM file being parsed.
| Version =    1.000 Date = 02/24/09 Time = 08:52:47
 NATOM  =     218 NTYPES =      12 NBONH =     102 MBONA  =     123
 NTHETH =     230 MTHETA =     169 NPHIH =     463 MPHIA  =     323
 NHPARM =       0 NPARM  =       0 NNB   =    1202 NRES   =      12
 NBONA  =     123 NTHETA =     169 NPHIA =     323 NUMBND =      27
 NUMANG =      57 NPTRA  =      40 NATYP =      21 NPHB   =       0
 IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real               14260
|     Hollerith           1322
|     Integer            31189
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              238 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

--------------------------------------------------------------------------------
   2.  CONTROL  DATA  FOR  THE  RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin    =       1, nmropt  =       0
     ifswitch=       0, fswitchbeta=  10.000
 mdread> no continuous cutoff will be used for non-bonded terms

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     =       2, nsnb    =      25
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     = 999.00000, intdiel =   1.00000
     saltcon =   0.20000, offset  =   0.09000, gbalpha=    0.80000
     gbbeta  =   0.00000, gbgamma =   2.90912, surften =   0.00500
     rdt     =   0.00000, rgbmax  =  25.00000
     alpb  =        0
     scnb    =   2.00000, scee    =   1.20000

Frozen or restrained atoms:
     ibelly  =       0, ntr     =       0

Energy minimization:
     maxcyc  =       1, ncyc    =       1, ntmin   =       1
     dx0     =   0.01000, drms    =   0.00010
|  INFO: Old style inpcrd file read


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

                                                                                
 begin time read from input coords =     0.000 ps

 Number of triangulated 3-point waters found:        0
 getparams> Number of atoms (or variables)  determined as    218
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=    25
read argument: coords.prmtop 
Reading parm file (coords.prmtop)
title:
                                                                                
 fetchz> Hybrid EF/BFGS transition state search, maximum steps= 250
         maximum tangent space steps=   5 or  100 when overlap is better than     0.999900
 fetchz> Uphill mode is    0 for initial step and    0 after that
 fetchz> Steps for largest Hessian e/vector= 100, smallest e/vector=2000 convergence at       0.0020%

 fetchz>  654 Cartesian coordinates will be optimised for  218 AMBER atoms

 fetchz> Lowest   1 eigenvalues and eigenvectors will be calculated non-iteratively
 fetchz> Point group checked when RMS force <     0.00100000, highest symmetry axis tested for=  6
 fetchz> Initial distance and eigenvalue tolerances in symmetry determination=     0.00010000     0.00010000
 fetchz> Minimum number of optimization steps=     0
 keywords> Cutoff for identifying atoms in the same orbit=    0.2000000000    
 keywords> lpermdist neighbours, threshold, max sep=    10     1.000000000         3
 fetchz> Convergence criterion for LBFGS optimization: RMS force< 0.10000000E-05 maximum steps= 10000
 fetchz> Maximum energy rise in LBFGS minimization=    0.1000000000E-01
 fetchz> Number of updates in LBFGS=    10000
 fetchz> Number of updates in XLBFGS=   4
 fetchz> Number of updates in mind=   4
 fetchz> Initial guess for diagonal elements in LBFGS=     0.0100
 fetchz> Initial guess for diagonal elements in XLBFGS=    0.1000
 fetchz> Maximum step size in LBFGS energy minimization=     0.1000
 fetchz> Maximum step size in XLBFGS=    0.2000
 fetchz> Maximum step size in LBFGS neb image minimization=                 0.2000
 fetchz> Warnings will be issued if atoms become closer than 0.5 units
 fetchz> Coordinates for intermediate steps will not be dumped to file points


 KeyInt>> Using natural internal coordinates. # of coords =        648
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         74      7440
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -446.5430051     RMS force=    0.8750426765E-06
 OPTIM> Final energy  =    -447.5328331     RMS force=    0.9090014710E-06
 KeyConnect> Maximum cycles = 50, maximum images = 23
 KeyConnect> Maximum attempts per pair of minima = 3, with increment image density of 2.00
 KeyConnect> Image density = 0.30, iteration density = 35.00
 KeyNEB> Initial and final NEB force constants     10.00000000        10.00000000     factor=    1.010000000    
 KeyNEB> Number of images will vary depending on the separation of the endpoints
 KeyGrad> Overall rotation and translation will NOT be removed
 KeyGrad> Using doubly nudged elastic band gradient
 KeyOutput> Transition state candidates will be optimized
 KeyOutput> Concise printing during transition states optimization
 KeyOutput> Transition state candidates are maxima along NEB
 KeyMin> Maximal number of iterations will vary, depending on the number of images in the band
 KeyMin> RMS convergence criterion is set to 0.001
 KeyMin> L-BFGS minimization
 KeyLBFGS> Maximum step size per image =     0.2000000000    
 KeyLBFGS> 4 Hessian updates per iteration
 KeyLBFGS> Guess for inverse Hessian diagonal elements =     0.1000000000E-02
 KeyTau> Using Henkelman and Jonsson's improved tangent
 KeyDecide> Cost function in Dijkstra algorithm is D^3

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     12668.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.31     1 
 

 tryconnect> 210-iteration DNEB run for minima 1_S and 2_F using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.2289 Dev= 0.68% S= 40.37 time= 9.66
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        100
 DNEB run yielded 1 true transition state(s) time=  62.85

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1953 steps. Energy=    -447.3031652       time=      34.08
 Minus side of path:                    1578 steps. Energy=    -447.6633929       time=      25.71

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.3031652  1.8293         -445.4739090  2.1895         -447.6633929  81.616  64.183   1.833 118.954
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     15562.    
 decide> The unconnected minima in the chain and their distances are:
     2        3.18     4     4       24.95     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1240 Dev= 0.23% S= 3.30 time= 1.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=  24.17

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1289 steps. Energy=    -447.6633929       time=      17.23
 Minus side of path:                    1275 steps. Energy=    -447.5328330       time=      17.13

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.6633929 0.89422         -446.7691716 0.76366         -447.5328330   3.285   3.182  16.497  13.215
        Known (#4)                                              Known (#2)
 Unconnected minimum 4 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 4_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.1802 Dev= 1.27% S= 42.78 time= 13.38
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time=  45.54

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1623 steps. Energy=    -446.4335975       time=      19.52
 Minus side of path:                    1307 steps. Energy=    -445.8957040       time=      14.28

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.4335975  1.3345         -445.0990806 0.79662         -445.8957040  42.722  38.374   2.650  82.270
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     25335.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.31     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.998725396    
 Double-ended search iterations= 805 RMS= 0.0730 Dev= 5.05% S= 56.74 time= 138.21
 Following    2 images are candidates for TS:    8   15  
 Converged to TS (number of iterations):         45
 Converged to TS (number of iterations):         82
 DNEB run yielded 2 true transition state(s) time=  88.74

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1299 steps. Energy=    -445.4178256       time=      14.10
 Minus side of path:                    1395 steps. Energy=    -446.9477859       time=      15.75

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.4178256  2.0614         -443.3563864  3.5914         -446.9477859  24.279  20.849   6.568  33.192
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    2127 steps. Energy=    -446.3179936       time=      30.14
 Minus side of path:                    2159 steps. Energy=    -445.8415769       time=      38.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.3179936  4.0319         -442.2861284  3.5554         -445.8415769  68.435  20.815  20.269  10.755
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 10 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     6549.6    
 decide> The unconnected minima in the chain and their distances are:
     2       15.94     8     8       13.57     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 8_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 140 RMS= 0.2660 Dev= 1.48% S= 18.00 time= 4.55
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=  36.31

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1274 steps. Energy=    -446.8907705       time=      17.86
 Minus side of path:                    1247 steps. Energy=    -446.9477859       time=      18.73

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.8907705 0.75696         -446.1338070 0.81398         -446.9477859   1.803   1.646 147.854   1.474
        *NEW* (Placed in 11)                                    Known (#8)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 1_S and 8_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0177 Dev= 0.06% S= 13.62 time= 4.47
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=  27.29

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1259 steps. Energy=    -446.5430051       time=      17.08
 Minus side of path:                    1299 steps. Energy=    -446.9477859       time=      17.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.5430051 0.32619         -446.2168135 0.73097         -446.9477859  13.666  13.567   3.557  61.286
        Known (#1)                                              Known (#8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     4132.3    
 decide> The unconnected minima in the chain and their distances are:
     2       16.05    11 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 11_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 140 RMS= 0.9498 Dev= 0.85% S= 18.23 time= 4.53
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        106
 DNEB run yielded 1 true transition state(s) time=  60.86

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1944 steps. Energy=    -449.0251467       time=      25.58
 Minus side of path:                    1525 steps. Energy=    -446.3065560       time=      17.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.0251467  8.6969         -440.3282547  5.9783         -446.3065560  63.078  44.814   2.663  81.850
        *NEW* (Placed in 12)                                    *NEW* (Placed in 13)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 13 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     4726.6    
 decide> The unconnected minima in the chain and their distances are:
     4       16.78     8 
 

 tryconnect> 175-iteration DNEB run for minima 4_F and 8_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 175 RMS= 0.3342 Dev= 1.20% S= 19.11 time= 6.82
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         95
 DNEB run yielded 1 true transition state(s) time=  60.31

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1608 steps. Energy=    -447.6633929       time=      21.79
 Minus side of path:                    1477 steps. Energy=    -446.9374024       time=      17.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.6633929  7.9942         -439.6691888  7.2682         -446.9374024  56.904  34.297   3.046  71.574
        Known (#4)                                              *NEW* (Placed in 14)
 Unconnected minimum 14 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 14 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     2213.1    
 decide> The unconnected minima in the chain and their distances are:
    14       13.03     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 14_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.1862 Dev= 0.07% S= 13.15 time= 2.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         53
 DNEB run yielded 1 true transition state(s) time=  42.09

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1323 steps. Energy=    -446.9374024       time=      18.78
 Minus side of path:                    1298 steps. Energy=    -446.5430051       time=      19.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.9374024 0.95186         -445.9855388 0.55747         -446.5430051  25.352  13.146   4.706  46.325
        Known (#14)                                             Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
  10     -446.5430051 0.55747        -445.9855388 0.95186        -446.9374024  25.352  13.146   4.706  46.325
   9     -446.9374024  7.2682        -439.6691888  7.9942        -447.6633929  56.904  34.297   3.046  71.574
   2     -447.6633929 0.89422        -446.7691716 0.76366        -447.5328331   3.285   3.182  16.497  13.215

 Number of TS in the path       =      3
 Number of cycles               =      7

 Elapsed time=                              1053.87
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             69342 time=         520.71 %= 49.4
 OPTIM> # of energy+gradient+Hessian calls=       643 time=         183.74 %= 17.4
