
 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 05/28/2012 at 09:47:15
  [-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 = 12/07/08 Time = 15:32:39
 NATOM  =     107 NTYPES =      11 NBONH =      48 MBONA  =      59
 NTHETH =     105 MTHETA =      79 NPHIH =     235 MPHIA  =     150
 NHPARM =       0 NPARM  =       0 NNB   =     560 NRES   =       7
 NBONA  =      59 NTHETA =      79 NPHIA =     150 NUMBND =      18
 NUMANG =      35 NPTRA  =      25 NATYP =      14 NPHB   =       0
 IFBOX  =       0 NMXRS  =      22 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real                7111
|     Hollerith            651
|     Integer            25418
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              157 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    107
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=    17
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>  321 Cartesian coordinates will be optimised for  107 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 =        315
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         65      3594
 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=    -532.0650985     RMS force=    0.9851353463E-06
 OPTIM> Final energy  =    -532.2773819     RMS force=    0.9550541939E-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=     7315.7    
 decide> The unconnected minima in the chain and their distances are:
     2       19.41     1 
 

 tryconnect> 175-iteration DNEB run for minima 1_S and 2_F using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.3533 Dev= 1.81% S= 23.24 time= 1.87
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         89
 DNEB run yielded 1 true transition state(s) time=   9.06

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     644 steps. Energy=    -530.7771366       time=       1.59
 Minus side of path:                     678 steps. Energy=    -532.0208651       time=       1.74

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.7771366  1.4472         -529.3299846  2.6909         -532.0208651  17.696  14.518   8.523  12.555
        *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=     7087.5    
 decide> The unconnected minima in the chain and their distances are:
     2       10.21     4     4       18.20     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 1.2671 Dev= 0.34% S= 15.98 time= 0.74
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         62
 DNEB run yielded 1 true transition state(s) time=   6.34

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     693 steps. Energy=    -530.4240851       time=       1.76
 Minus side of path:                     699 steps. Energy=    -532.2773819       time=       1.79

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.4240851  1.0137         -529.4104119  2.8670         -532.2773819  20.544  17.471   7.947  13.465
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 1_S and 4_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.5217 Dev= 0.45% S= 19.11 time= 1.87
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         36
 DNEB run yielded 1 true transition state(s) time=   4.58

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     674 steps. Energy=    -532.0650985       time=       1.75
 Minus side of path:                     655 steps. Energy=    -532.2773819       time=       1.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.0650985  1.0707         -530.9944054  1.2830         -532.2773819  19.474  17.011   2.189  48.878
        Known (#1)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     974.14    
 decide> The unconnected minima in the chain and their distances are:
     2        9.91     6 
 

 checkpair> Energies of the minima in the pair     2    6 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 1.3992 Dev= 1.39% S= 15.46 time= 0.38
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):        136
 DNEB run yielded 1 true transition state(s) time=  23.15
 isnewts> transition state is the same as number        2 energy=     -529.4104119115
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     670 steps. Energy=    -532.2773819       time=       1.70
 Minus side of path:                     683 steps. Energy=    -530.4240851       time=       1.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.2773819  2.8670         -529.4104119  1.0137         -530.4240851  20.543  17.470   7.961  13.440
        Known (#2)                                              Known (#5)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     1384.3    
 decide> The unconnected minima in the chain and their distances are:
     5       11.09     3     4        2.69     6 
 

 tryconnect> 105-iteration DNEB run for minima 3_U and 5_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.7114 Dev= 0.37% S= 16.60 time= 0.73
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         80
 DNEB run yielded 1 true transition state(s) time=   7.81

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     623 steps. Energy=    -530.7771366       time=       1.52
 Minus side of path:                     645 steps. Energy=    -532.4786512       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.7771366 0.11002         -530.6671141  1.8115         -532.4786512   9.506   8.748   2.266  47.227
        Known (#3)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_U and 6_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 0.3115 Dev= 1.69% S= 3.25 time= 0.38
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         94
 DNEB run yielded 1 true transition state(s) time=   8.95

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     626 steps. Energy=    -532.2773819       time=       1.55
 Minus side of path:                     630 steps. Energy=    -532.4757719       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.2773819 0.40588         -531.8714987 0.60427         -532.4757719   8.581   7.804   3.087  34.656
        Known (#6)                                              *NEW* (Placed in 8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     1333.2    
 decide> The unconnected minima in the chain and their distances are:
     5       10.90     7     4        2.69     6 
 

 tryconnect> 105-iteration DNEB run for minima 5_F and 7_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3258 Dev= 0.18% S= 13.90 time= 0.74
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         59
 DNEB run yielded 1 true transition state(s) time=   6.09

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     738 steps. Energy=    -532.3570695       time=       1.87
 Minus side of path:                     665 steps. Energy=    -531.8541018       time=       1.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.3570695  3.3874         -528.9696697  2.8844         -531.8541018  18.542  10.559  13.193   8.110
        *NEW* (Placed in 9)                                     *NEW* (Placed in 10)
 Connection established between members of the U set.

 tryconnect> 210-iteration DNEB run for minima 4_U and 6_S using 6 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.0517 Dev= 2.75% S= 3.93 time= 2.64
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         10
 DNEB run yielded 1 true transition state(s) time=   2.21

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     630 steps. Energy=    -532.0208651       time=       1.54
 Minus side of path:                     632 steps. Energy=    -532.2773819       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.0208651  8.3295         -523.6913320  8.5860         -532.2773819   3.069   2.687  49.110   2.179
        Known (#4)                                              Known (#6)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      8 steps with      2 missing connections, weight=     768.30    
 decide> The unconnected minima in the chain and their distances are:
     5        8.69    10     9        4.82     7 
 

 tryconnect> 70-iteration DNEB run for minima 5_F and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.5144 Dev= 0.02% S= 8.77 time= 0.38
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=   4.42

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     699 steps. Energy=    -531.8541018       time=       1.75
 Minus side of path:                     590 steps. Energy=    -530.4240851       time=       1.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.8541018  1.4319         -530.4222078 0.18772E-02     -530.4240851   8.769   8.692   1.997  53.582
        Known (#10)                                             Known (#5)
 Unconnected minimum 10 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 7_S and 9_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 7.5486 Dev= 0.88% S= 4.88 time= 0.38
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   4.05

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     618 steps. Energy=    -532.3570695       time=       1.51
 Minus side of path:                     611 steps. Energy=    -532.4786512       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.3570695 0.43679E-01     -532.3133901 0.16526         -532.4786512   5.464   4.817   2.154  49.670
        Known (#9)                                              Known (#7)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   3     -532.0650985  1.0707        -530.9944054  1.2830        -532.2773819  19.474  17.011   2.189  48.878
   8     -532.2773819  8.5860        -523.6913320  8.3295        -532.0208651   3.069   2.687  49.110   2.179
   1     -532.0208651  2.6909        -529.3299846  1.4472        -530.7771366  17.696  14.518   8.523  12.555
   5     -530.7771366 0.11002        -530.6671141  1.8115        -532.4786512   9.506   8.748   2.266  47.227
  10     -532.4786512 0.16526        -532.3133901 0.43679E-01    -532.3570695   5.464   4.817   2.154  49.670
   7     -532.3570695  3.3874        -528.9696697  2.8844        -531.8541018  18.542  10.559  13.193   8.110
   9     -531.8541018  1.4319        -530.4222078 0.18772E-02    -530.4240851   8.769   8.692   1.997  53.582
   2     -530.4240851  1.0137        -529.4104119  2.8670        -532.2773819  20.544  17.471   7.947  13.465

 Number of TS in the path       =      8
 Number of cycles               =      6

 Elapsed time=                               120.20
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             26575 time=          53.11 %= 44.2
 OPTIM> # of energy+gradient+Hessian calls=       637 time=          34.75 %= 28.9
