
 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 05/24/2012 at 21:03:40
  [-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.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -453.0685383     RMS force=    0.9502767284E-06
 OPTIM> Final energy  =    -454.0602536     RMS force=    0.9990932197E-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=    0.16677E+06
 decide> The unconnected minima in the chain and their distances are:
     2       55.04     1 
 

 tryconnect> 560-iteration DNEB run for minima 1_S and 2_F using 16 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2224511589    
 Double-ended search iterations= 560 RMS= 0.0638 Dev= 6.31% S= 70.63 time= 67.79
 Following    3 images are candidates for TS:    7    9   11  
 Converged to TS (number of iterations):         83
 Converged to TS (number of iterations):        221
 Converged to TS (number of iterations):        212
 DNEB run yielded 3 true transition state(s) time= 288.31

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1273 steps. Energy=    -453.9906852       time=      13.05
 Minus side of path:                    1268 steps. Energy=    -453.0685383       time=      12.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.9906852  1.0711         -452.9195970 0.14894         -453.0685383  11.722  10.940   3.316  65.744
        *NEW* (Placed in 3)                                     Known (#1)
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1138 steps. Energy=    -456.4696132       time=      11.18
 Minus side of path:                    1172 steps. Energy=    -457.9156941       time=      11.66

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -456.4696132  1.7329         -454.7366701  3.1790         -457.9156941  26.219  25.161   2.537  85.937
        *NEW* (Placed in 4)                                     *NEW* (Placed in 5)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1220 steps. Energy=    -453.2359634       time=      12.30
 Minus side of path:                    2033 steps. Energy=    -459.7633099       time=      26.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.2359634  2.2869         -450.9490634  8.8142         -459.7633099  65.869  61.418   1.670 130.557
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     27962.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.09     7     6       23.00     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 7_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0849 Dev= 1.99% S= 28.46 time= 13.05
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        109
 DNEB run yielded 1 true transition state(s) time=  54.76

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1156 steps. Energy=    -459.7633099       time=      11.47
 Minus side of path:                    1046 steps. Energy=    -457.0038270       time=      10.01

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -459.7633099  5.8735         -453.8897828  3.1140         -457.0038270  27.497  17.957   8.305  26.249
        Known (#7)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 1_S and 6_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.4765 Dev= 0.38% S= 24.03 time= 9.63
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         64
 DNEB run yielded 1 true transition state(s) time=  38.39

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1212 steps. Energy=    -453.8690522       time=      12.20
 Minus side of path:                    1379 steps. Energy=    -453.9906852       time=      14.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.8690522  1.1580         -452.7110376  1.2796         -453.9906852  25.777  23.508   5.118  42.595
        *NEW* (Placed in 9)                                     Known (#3)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     27255.    
 decide> The unconnected minima in the chain and their distances are:
     2       29.59     8     6       11.08     9 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 8_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0776 Dev= 1.65% S= 33.45 time= 16.96
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         87
 DNEB run yielded 1 true transition state(s) time=  47.94

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1037 steps. Energy=    -453.6863785       time=       9.86
 Minus side of path:                    1016 steps. Energy=    -453.5654829       time=       9.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.6863785 0.23311         -453.4532671 0.11222         -453.5654829   3.303   3.093   4.043  53.917
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 6_U and 9_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 2.8333 Dev= 0.59% S= 11.25 time= 2.60
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=  25.85

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1230 steps. Energy=    -453.8690523       time=      12.44
 Minus side of path:                    1202 steps. Energy=    -453.2359634       time=      12.04

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.8690523 0.98773         -452.8813246 0.35464         -453.2359634  13.560  11.078   4.649  46.893
        Known (#9)                                              Known (#6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 11 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     16204.    
 decide> The unconnected minima in the chain and their distances are:
     2       22.75    11    11       16.41     7 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 11_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.2007 Dev= 0.90% S= 24.36 time= 9.66
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=  27.92

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1118 steps. Energy=    -453.2989139       time=      10.92
 Minus side of path:                    1156 steps. Energy=    -454.4860104       time=      11.42

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.2989139 0.19923         -453.0996836  1.3863         -454.4860104  14.441  13.841   2.961  73.619
        *NEW* (Placed in 12)                                    *NEW* (Placed in 13)
 Connection established between members of the U set.

 tryconnect> 140-iteration DNEB run for minima 7_S and 11_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 1.4849 Dev= 0.83% S= 17.38 time= 4.44
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         48
 DNEB run yielded 1 true transition state(s) time=  29.54

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1131 steps. Energy=    -459.6505365       time=      11.10
 Minus side of path:                    1064 steps. Energy=    -453.6863785       time=      10.20

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -459.6505365  6.5291         -453.1214275 0.56495         -453.6863785  17.585  14.200   5.678  38.393
        *NEW* (Placed in 14)                                    Known (#10)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 14 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      3 missing connections, weight=     2970.2    
 decide> The unconnected minima in the chain and their distances are:
     2       12.23    13    12        9.67    11    14        6.21     7 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 13_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0924 Dev= 0.05% S= 12.27 time= 2.60
 Following    1 images are candidates for TS:    2  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 117.60

 tryconnect> 70-iteration DNEB run for minima 11_U and 12_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0584 Dev= 0.01% S= 9.68 time= 1.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         40
 DNEB run yielded 1 true transition state(s) time=  26.34

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                    1123 steps. Energy=    -453.5654829       time=      10.98
 Minus side of path:                    1020 steps. Energy=    -453.2989139       time=       9.63

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.5654829 0.29092         -453.2745633 0.24351E-01     -453.2989139  10.445   9.671   2.713  80.343
        Known (#11)                                             Known (#12)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 7_S and 14_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0261 Dev= 0.01% S= 6.21 time= 1.30
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         15
 DNEB run yielded 1 true transition state(s) time=  13.54

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     850 steps. Energy=    -459.6505365       time=       7.58
 Minus side of path:                     913 steps. Energy=    -459.7633099       time=       8.33

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -459.6505365 0.53347E-02     -459.6452018 0.11811         -459.7633099   6.228   6.206   7.671  28.417
        Known (#14)                                             Known (#7)
 Unconnected minimum 14 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 14 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has     10 steps with      1 missing connections, weight=     3655.1    
 decide> The unconnected minima in the chain and their distances are:
     2       12.23    13 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 13_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.227044011    
 Double-ended search iterations= 805 RMS= 0.0078 Dev= 4.75% S= 14.97 time= 138.24
 Following    2 images are candidates for TS:    5   13  
 Converged to TS (number of iterations):         15
 Converged to TS (number of iterations):         16
 DNEB run yielded 2 true transition state(s) time=  33.08

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                    1125 steps. Energy=    -454.5458678       time=      10.99
 Minus side of path:                    1081 steps. Energy=    -454.0602536       time=      10.40

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.5458678 0.56673         -453.9791412 0.81112E-01     -454.0602536   7.856   6.429   3.453  63.138
        *NEW* (Placed in 15)                                    Known (#2)
 Unconnected minimum 15 found its way to F set.

 >>>>>  Path run for ts 13 ...
 Plus  side of path:                    1138 steps. Energy=    -454.4860104       time=      11.17
 Minus side of path:                    1129 steps. Energy=    -454.5458678       time=      11.07

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.4860104 0.46451         -454.0214960 0.52437         -454.5458678  13.527  13.089   2.976  73.255
        Known (#13)                                             Known (#15)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -453.0685383 0.14894        -452.9195970  1.0711        -453.9906852  11.722  10.940   3.316  65.744
   5     -453.9906852  1.2796        -452.7110376  1.1580        -453.8690522  25.777  23.508   5.118  42.595
   7     -453.8690522 0.98773        -452.8813246 0.35464        -453.2359634  13.560  11.078   4.649  46.893
   3     -453.2359634  2.2869        -450.9490634  8.8142        -459.7633099  65.869  61.418   1.670 130.557
  11     -459.7633099 0.11811        -459.6452018 0.53347E-02    -459.6505365   6.228   6.206   7.671  28.417
   9     -459.6505365  6.5291        -453.1214275 0.56495        -453.6863785  17.585  14.200   5.678  38.393
   6     -453.6863785 0.23311        -453.4532671 0.11222        -453.5654829   3.303   3.093   4.043  53.917
  10     -453.5654829 0.29092        -453.2745633 0.24351E-01    -453.2989139  10.445   9.671   2.713  80.343
   8     -453.2989139 0.19923        -453.0996836  1.3863        -454.4860104  14.441  13.841   2.961  73.619
  13     -454.4860104 0.46451        -454.0214960 0.52437        -454.5458678  13.527  13.089   2.976  73.255
  12     -454.5458678 0.56673        -453.9791412 0.81112E-01    -454.0602536   7.856   6.429   3.453  63.138

 Number of TS in the path       =     11
 Number of cycles               =      6

 Elapsed time=                              1275.57
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             83634 time=         619.70 %= 48.6
 OPTIM> # of energy+gradient+Hessian calls=      1235 time=         350.11 %= 27.4
