
 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 11:02:34
  [-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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -533.4986140     RMS force=    0.7409726325E-06
 OPTIM> Final energy  =    -531.7254312     RMS force=    0.8034864820E-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=     4478.5    
 decide> The unconnected minima in the chain and their distances are:
     2       16.48     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 140 RMS= 0.4820 Dev= 0.44% S= 18.64 time= 1.15
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         70
 DNEB run yielded 1 true transition state(s) time=   7.65

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     631 steps. Energy=    -532.3643097       time=       1.60
 Minus side of path:                     624 steps. Energy=    -536.0967470       time=       1.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.3643097 0.66656         -531.6977538  4.3990         -536.0967470   9.829   8.781   2.558  41.836
        *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=     3290.7    
 decide> The unconnected minima in the chain and their distances are:
     2       14.10     4     4        7.88     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 4_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 140 RMS= 0.6440 Dev= 0.90% S= 16.27 time= 1.16
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        200
 DNEB run yielded 1 true transition state(s) time=  22.46

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     601 steps. Energy=    -528.4124457       time=       1.78
 Minus side of path:                     918 steps. Energy=    -531.3777168       time=       3.26

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -528.4124457 0.16562         -528.2468258  3.1309         -531.3777168  14.141  12.783   5.278  20.271
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 4_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.3149 Dev= 0.18% S= 8.39 time= 0.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         34
 DNEB run yielded 1 true transition state(s) time=   4.55

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     704 steps. Energy=    -536.0967470       time=       1.83
 Minus side of path:                     581 steps. Energy=    -533.5989010       time=       1.47

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0967470  2.6579         -533.4388756 0.16003         -533.5989010   6.703   6.200  10.135  10.557
        Known (#4)                                              *NEW* (Placed in 7)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 7 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     3508.1    
 decide> The unconnected minima in the chain and their distances are:
     2       15.11     7     7        3.94     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 7_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 140 RMS= 0.3792 Dev= 1.57% S= 17.38 time= 1.17
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time=   8.46

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     602 steps. Energy=    -536.0967470       time=       1.50
 Minus side of path:                     604 steps. Energy=    -534.7245694       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0967470  3.7875         -532.3092154  2.4154         -534.7245694   7.768   6.974   8.606  12.434
        Known (#4)                                              *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1100 Dev= 0.04% S= 3.97 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         18
 DNEB run yielded 1 true transition state(s) time=   2.69

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     565 steps. Energy=    -533.5989010       time=       1.37
 Minus side of path:                     563 steps. Energy=    -533.4986140       time=       1.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.5989010 0.24513         -533.3537749 0.14484         -533.4986140   4.086   3.942  10.446  10.243
        Known (#7)                                              Known (#1)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 8 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1807.5    
 decide> The unconnected minima in the chain and their distances are:
     2       12.18     8 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 8_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.4354 Dev= 1.82% S= 14.10 time= 0.63
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        234
 DNEB run yielded 1 true transition state(s) time=  22.52

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     751 steps. Energy=    -534.7245694       time=       2.05
 Minus side of path:                     634 steps. Energy=    -534.9933182       time=       1.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -534.7245694  1.1281         -533.5964482  1.3969         -534.9933182  15.048  12.381   6.707  15.954
        Known (#8)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     3615.0    
 decide> The unconnected minima in the chain and their distances are:
     2       12.18     8 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 8_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.1300625854    
 Double-ended search iterations= 805 RMS= 0.0103 Dev= 4.51% S= 22.62 time= 37.99
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         14
 DNEB run yielded 1 true transition state(s) time=   2.95

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     907 steps. Energy=    -538.2010919       time=       2.50
 Minus side of path:                     772 steps. Energy=    -534.7245694       time=       1.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.2010919  10.035         -528.1664538  6.5581         -534.7245694  30.831  19.345   4.135  25.879
        *NEW* (Placed in 10)                                    Known (#8)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 10 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     4048.2    
 decide> The unconnected minima in the chain and their distances are:
     2       15.94     3 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.2538 Dev= 0.17% S= 16.94 time= 1.13
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=   3.99

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     632 steps. Energy=    -532.3643097       time=       1.58
 Minus side of path:                     592 steps. Energy=    -530.3826615       time=       1.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -532.3643097  3.7326         -528.6317092  1.7510         -530.3826615   7.887   6.786   8.266  12.945
        Known (#3)                                              *NEW* (Placed in 11)
 Unconnected minimum 11 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 11 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     2899.7    
 decide> The unconnected minima in the chain and their distances are:
     2       14.26    11 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 11_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.1526 Dev= 0.12% S= 15.02 time= 1.13
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         32
 DNEB run yielded 1 true transition state(s) time=   4.03

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     726 steps. Energy=    -531.3777168       time=       1.86
 Minus side of path:                     637 steps. Energy=    -531.7254312       time=       1.58

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.3777168  2.1303         -529.2473779  2.4781         -531.7254312  18.473  15.557   4.629  23.114
        Known (#6)                                              Known (#2)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 11 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     794.97    
 decide> The unconnected minima in the chain and their distances are:
     6        9.26    11 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 11_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1902 Dev= 0.08% S= 9.37 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=   3.89

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     654 steps. Energy=    -531.6135310       time=       1.66
 Minus side of path:                     582 steps. Energy=    -530.3826615       time=       1.43

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.6135310  1.3939         -530.2196452 0.16302         -530.3826615   8.430   7.832   2.062  51.890
        *NEW* (Placed in 12)                                    Known (#11)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 12 minima and 10 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     111.39    
 decide> The unconnected minima in the chain and their distances are:
     6        4.81    12 
 

 tryconnect> 70-iteration DNEB run for minima 6_F and 12_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1351 Dev= 0.09% S= 4.91 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   2.85

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     596 steps. Energy=    -531.3777168       time=       1.46
 Minus side of path:                     602 steps. Energy=    -531.6135310       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -531.3777168 0.42484E-01     -531.3352327 0.27830         -531.6135310   5.026   4.812  13.621   7.856
        Known (#6)                                              Known (#12)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -533.4986140 0.14484        -533.3537749 0.24513        -533.5989010   4.086   3.942  10.446  10.243
   3     -533.5989010 0.16003        -533.4388756  2.6579        -536.0967470   6.703   6.200  10.135  10.557
   1     -536.0967470  4.3990        -531.6977538 0.66656        -532.3643097   9.829   8.781   2.558  41.836
   8     -532.3643097  3.7326        -528.6317092  1.7510        -530.3826615   7.887   6.786   8.266  12.945
  10     -530.3826615 0.16302        -530.2196452  1.3939        -531.6135310   8.430   7.832   2.062  51.890
  11     -531.6135310 0.27830        -531.3352327 0.42484E-01    -531.3777168   5.026   4.812  13.621   7.856
   9     -531.3777168  2.1303        -529.2473779  2.4781        -531.7254312  18.473  15.557   4.629  23.114

 Number of TS in the path       =      7
 Number of cycles               =      9

 Elapsed time=                               170.63
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             45854 time=          92.63 %= 54.3
 OPTIM> # of energy+gradient+Hessian calls=       760 time=          42.82 %= 25.1
