
 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 09:41:50
  [-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=    -530.3182910     RMS force=    0.9981593642E-06
 OPTIM> Final energy  =    -528.3235516     RMS force=    0.9726301709E-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=     4074.1    
 decide> The unconnected minima in the chain and their distances are:
     2       15.97     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.462153966    
 Double-ended search iterations= 140 RMS= 0.9216 Dev= 1.31% S= 20.39 time= 1.14
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         79
 DNEB run yielded 1 true transition state(s) time=   7.73

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     578 steps. Energy=    -530.1691293       time=       1.43
 Minus side of path:                     603 steps. Energy=    -529.7855422       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.1691293  2.3498         -527.8193762  1.9662         -529.7855422  12.394  10.887  17.939   5.965
        *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      3 steps with      2 missing connections, weight=     2094.6    
 decide> The unconnected minima in the chain and their distances are:
     2       12.56     4     3        4.82     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 4_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 105 RMS= 5.8542 Dev= 1.63% S= 17.43 time= 0.55
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        207
 DNEB run yielded 1 true transition state(s) time=  19.64

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     709 steps. Energy=    -533.4986140       time=       1.81
 Minus side of path:                     586 steps. Energy=    -530.7044326       time=       1.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -533.4986140  2.9085         -530.5901112 0.11432         -530.7044326   8.082   7.395   3.155  33.918
        *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 3_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4190 Dev= 0.16% S= 5.38 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         90
 DNEB run yielded 1 true transition state(s) time=   9.50

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     725 steps. Energy=    -530.1691293       time=       1.87
 Minus side of path:                     798 steps. Energy=    -531.9253418       time=       2.10

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.1691293  1.5225         -528.6466608  3.2787         -531.9253418  22.643  19.499   3.670  29.153
        Known (#3)                                              *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=     3629.4    
 decide> The unconnected minima in the chain and their distances are:
     2       15.04     3     3        4.82     1 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      11.02500000    
 Double-ended search iterations= 140 RMS= 1.4541 Dev= 0.89% S= 19.56 time= 1.13
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         82
 DNEB run yielded 1 true transition state(s) time=   8.09

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     600 steps. Energy=    -530.3182910       time=       1.49
 Minus side of path:                     742 steps. Energy=    -530.5350581       time=       1.92

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.3182910  2.4602         -527.8580833  2.6770         -530.5350581  17.051  12.849  12.371   8.649
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.

 tryconnect> 385-iteration DNEB run for minima 1_S and 3_U using 11 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.203594749    
 Double-ended search iterations= 385 RMS= 0.1118 Dev= 0.62% S= 6.44 time= 8.59
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):          8
 DNEB run yielded 1 true transition state(s) time=   2.02

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     576 steps. Energy=    -530.1691293       time=       1.42
 Minus side of path:                     570 steps. Energy=    -530.3182910       time=       1.41

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.1691293  8.3788         -521.7902893  8.5280         -530.3182910   5.140   4.823  19.454   5.500
        Known (#3)                                              Known (#1)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 9 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     3180.9    
 decide> The unconnected minima in the chain and their distances are:
     2       13.02     8     8        9.91     1 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 8_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3532 Dev= 0.10% S= 13.45 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=   5.37
 isnewts> transition state is the same as number        4 energy=     -527.8580832834
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 6 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     736 steps. Energy=    -530.5350581       time=       1.90
 Minus side of path:                     596 steps. Energy=    -530.3182910       time=       1.48

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.5350581  2.6770         -527.8580833  2.4602         -530.3182910  17.045  12.838  12.501   8.560
        Known (#9)                                              Known (#8)
 Connection established between members of the U set.

 checkpair> Energies of the minima in the pair     1    8 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 1_S and 8_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      9.070294785    
 Double-ended search iterations= 70 RMS= 4.6446 Dev= 3.22% S= 14.33 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=   5.41

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     683 steps. Energy=    -530.1691293       time=       1.73
 Minus side of path:                     608 steps. Energy=    -530.3182910       time=       1.51

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.1691293  4.5189         -525.6502778  4.6680         -530.3182910  18.160  11.011  14.313   7.476
        Known (#3)                                              Known (#8)
 Unconnected minimum 8 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     2534.0    
 decide> The unconnected minima in the chain and their distances are:
     2       13.63     9 
 

 tryconnect> 140-iteration DNEB run for minima 2_F and 9_S using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.418498711    
 Double-ended search iterations= 140 RMS= 0.2327 Dev= 1.46% S= 15.21 time= 1.14
 Following    1 images are candidates for TS:    1  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time=  22.32
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     3145.1    
 decide> The unconnected minima in the chain and their distances are:
     2       12.21     5     5       10.98     9 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 5_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.303213506    
 Double-ended search iterations= 105 RMS= 0.5967 Dev= 0.56% S= 13.69 time= 0.64
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=   5.29

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     859 steps. Energy=    -530.5852566       time=       2.30
 Minus side of path:                     601 steps. Energy=    -529.5142732       time=       1.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.5852566  2.0094         -528.5758278 0.93845         -529.5142732  16.739  14.078   2.570  41.639
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 5_U and 9_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.3353 Dev= 0.48% S= 11.81 time= 0.64
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         95
 DNEB run yielded 1 true transition state(s) time=   8.97

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     591 steps. Energy=    -530.5350581       time=       1.47
 Minus side of path:                     722 steps. Energy=    -531.0960020       time=       1.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.5350581  1.1023         -529.4327267  1.6633         -531.0960020  13.161  12.354   1.831  58.434
        Known (#9)                                              *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 12 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      2 missing connections, weight=     355.25    
 decide> The unconnected minima in the chain and their distances are:
     2        6.48    11    10        4.36     9 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 11_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1917 Dev= 0.17% S= 6.65 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         23
 DNEB run yielded 1 true transition state(s) time=   3.25
 isnewts> transition state is the same as number        8 energy=     -528.5758278271
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 10 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                     859 steps. Energy=    -530.5852566       time=       2.30
 Minus side of path:                     624 steps. Energy=    -529.5142732       time=       1.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.5852566  2.0094         -528.5758278 0.93845         -529.5142732  16.739  14.077   2.575  41.551
        Known (#10)                                             Known (#11)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 9_S and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1214 Dev= 0.02% S= 4.51 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         17
 DNEB run yielded 1 true transition state(s) time=   2.66

 >>>>>  Path run for ts 11 ...
 Plus  side of path:                     556 steps. Energy=    -530.5350581       time=       1.36
 Minus side of path:                     585 steps. Energy=    -530.5852566       time=       1.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.5350581 0.34028E-01     -530.5010301 0.84227E-01     -530.5852566   4.528   4.361  12.409   8.623
        Known (#9)                                              Known (#10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 12 minima and 11 ts are known >>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     544.68    
 decide> The unconnected minima in the chain and their distances are:
     2        6.48    11 
 

 tryconnect> 490-iteration DNEB run for minima 2_F and 11_S using 14 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.903547996    
 Double-ended search iterations= 490 RMS= 0.0291 Dev= 14.42% S= 7.57 time= 13.87
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         12
 DNEB run yielded 1 true transition state(s) time=   2.21

 >>>>>  Path run for ts 12 ...
 Plus  side of path:                     899 steps. Energy=    -530.5852566       time=       2.39
 Minus side of path:                     541 steps. Energy=    -528.3235516       time=       1.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -530.5852566  2.2658         -528.3195052 0.40464E-02     -528.3235516  14.965  14.509   3.534  30.277
        Known (#10)                                             Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -530.3182910  8.5280        -521.7902893  8.3788        -530.1691293   5.140   4.823  19.454   5.500
   7     -530.1691293  4.5189        -525.6502778  4.6680        -530.3182910  18.160  11.011  14.313   7.476
   4     -530.3182910  2.4602        -527.8580833  2.6770        -530.5350581  17.051  12.849  12.371   8.649
  11     -530.5350581 0.34028E-01    -530.5010301 0.84227E-01    -530.5852566   4.528   4.361  12.409   8.623
  12     -530.5852566  2.2658        -528.3195052 0.40464E-02    -528.3235516  14.965  14.509   3.534  30.277

 Number of TS in the path       =      5
 Number of cycles               =      8

 Elapsed time=                               173.59
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             40674 time=          81.78 %= 47.1
 OPTIM> # of energy+gradient+Hessian calls=      1014 time=          55.30 %= 31.9
