
 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 09:39:44
  [-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=    -537.7713546     RMS force=    0.9998233365E-06
 OPTIM> Final energy  =    -537.7085083     RMS force=    0.9370835789E-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=     4516.5    
 decide> The unconnected minima in the chain and their distances are:
     2       16.53     1 
 

 tryconnect> 140-iteration DNEB run for minima 1_S and 2_F using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      4.155206549    
 Double-ended search iterations= 140 RMS= 0.6304 Dev= 0.50% S= 20.42 time= 1.13
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         65
 DNEB run yielded 1 true transition state(s) time=   6.57

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                     668 steps. Energy=    -536.6999265       time=       1.68
 Minus side of path:                     727 steps. Energy=    -537.2783242       time=       1.87

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.6999265  4.0927         -532.6072066  4.6711         -537.2783242  20.803  16.319   4.546  23.535
        *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=     7224.0    
 decide> The unconnected minima in the chain and their distances are:
     2       17.82     3     3       11.62     1 
 

 tryconnect> 175-iteration DNEB run for minima 2_F and 3_U using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.1496 Dev= 1.05% S= 19.12 time= 1.77
 Following    2 images are candidates for TS:    2    4  
 Converged to TS (number of iterations):         46
 Converged to TS (number of iterations):         38
 DNEB run yielded 2 true transition state(s) time=   9.47

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                     819 steps. Energy=    -536.8666959       time=       2.14
 Minus side of path:                     882 steps. Energy=    -538.4403292       time=       2.35

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.8666959 0.53739         -536.3293041  2.1110         -538.4403292  20.211  13.436   2.695  39.697
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                     636 steps. Energy=    -536.0954362       time=       1.58
 Minus side of path:                     726 steps. Energy=    -537.3889952       time=       1.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.0954362  1.1436         -534.9518000  2.4372         -537.3889952  18.723  17.355   3.970  26.951
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 3_U using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.638375985    
 Double-ended search iterations= 105 RMS= 1.0411 Dev= 0.65% S= 16.39 time= 0.59
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):        134
 DNEB run yielded 1 true transition state(s) time=  12.19

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                     802 steps. Energy=    -536.6999265       time=       2.11
 Minus side of path:                     590 steps. Energy=    -535.2212308       time=       1.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -536.6999265  1.8013         -534.8986409 0.32259         -535.2212308  11.574  10.893   3.167  33.789
        Known (#3)                                              *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 9 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     1916.5    
 decide> The unconnected minima in the chain and their distances are:
     2        4.87     5     6       12.17     1 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 5_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4500 Dev= 0.01% S= 4.88 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         24
 DNEB run yielded 1 true transition state(s) time=   3.24

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                     579 steps. Energy=    -537.7085083       time=       1.44
 Minus side of path:                     564 steps. Energy=    -536.8666959       time=       1.39

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.7085083 0.85234         -536.8561663 0.10530E-01     -536.8666959   5.038   4.871   4.701  22.761
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 105-iteration DNEB run for minima 1_S and 6_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.106813301    
 Double-ended search iterations= 105 RMS= 0.8641 Dev= 0.70% S= 17.10 time= 0.57
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         68
 DNEB run yielded 1 true transition state(s) time=   6.85

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                     615 steps. Energy=    -538.4403292       time=       1.54
 Minus side of path:                     624 steps. Energy=    -538.0300290       time=       1.57

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.4403292  3.6481         -534.7921804  3.2378         -538.0300290  15.956  12.875   4.780  22.386
        *NEW* (Placed in 10)                                    *NEW* (Placed in 11)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 11 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     1328.0    
 decide> The unconnected minima in the chain and their distances are:
     6        9.91    10    10        7.07     1 
 

 checkpair> Energies of the minima in the pair     6   10 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 6_F and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 5.7697 Dev= 1.22% S= 14.02 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         64
 DNEB run yielded 1 true transition state(s) time=   6.44

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                     623 steps. Energy=    -538.4403292       time=       1.57
 Minus side of path:                     637 steps. Energy=    -538.0300290       time=       1.61

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.4403292  3.6481         -534.7921804  3.2378         -538.0300290  15.956  12.875   4.780  22.383
        Known (#6)                                              *NEW* (Placed in 12)
 Unconnected minimum 12 found its way to F set.

 tryconnect> 70-iteration DNEB run for minima 1_S and 10_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.4592 Dev= 0.25% S= 7.36 time= 0.29
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         20
 DNEB run yielded 1 true transition state(s) time=   2.95

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                     581 steps. Energy=    -537.7713546       time=       1.44
 Minus side of path:                     727 steps. Energy=    -538.4403292       time=       1.90

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -537.7713546 0.74634E-01     -537.6967209 0.74361         -538.4403292   7.690   7.076   5.381  19.886
        Known (#1)                                              Known (#10)
 Unconnected minimum 10 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 12 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     974.09    
 decide> The unconnected minima in the chain and their distances are:
    12        9.91    11 
 

 checkpair> Energies of the minima in the pair    11   12 are the same - checking distance ...

 tryconnect> 70-iteration DNEB run for minima 11_S and 12_F using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      8.227024748    
 Double-ended search iterations= 70 RMS= 4.1494 Dev= 3.87% S= 14.28 time= 0.29
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         31
 DNEB run yielded 1 true transition state(s) time=   3.93

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                     606 steps. Energy=    -538.0600999       time=       1.52
 Minus side of path:                     614 steps. Energy=    -538.0300290       time=       1.54

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.0600999  8.7093         -529.3508410  8.6792         -538.0300290   2.451   1.834  91.809   1.165
        *NEW* (Placed in 13)                                    Known (#12)
 Unconnected minimum 13 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 13 minima and 9 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      7 steps with      1 missing connections, weight=     1023.4    
 decide> The unconnected minima in the chain and their distances are:
    13       10.08    11 
 

 tryconnect> 105-iteration DNEB run for minima 11_S and 13_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      7.835261665    
 Double-ended search iterations= 105 RMS= 3.4298 Dev= 0.82% S= 15.52 time= 0.55
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=   3.74

 >>>>>  Path run for ts 10 ...
 Plus  side of path:                     682 steps. Energy=    -538.0300290       time=       1.72
 Minus side of path:                     748 steps. Energy=    -538.0600999       time=       1.93

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -538.0300290  4.9110         -533.1190209  4.9411         -538.0600999  20.188  10.168  15.382   6.956
        Known (#11)                                             Known (#13)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -537.7713546 0.74634E-01    -537.6967209 0.74361        -538.4403292   7.690   7.076   5.381  19.886
   6     -538.4403292  3.6481        -534.7921804  3.2378        -538.0300290  15.956  12.875   4.780  22.386
  10     -538.0300290  4.9110        -533.1190209  4.9411        -538.0600999  20.188  10.168  15.382   6.956
   9     -538.0600999  8.7093        -529.3508410  8.6792        -538.0300290   2.451   1.834  91.809   1.165
   7     -538.0300290  3.2378        -534.7921804  3.6481        -538.4403292  15.956  12.875   4.780  22.383
   2     -538.4403292  2.1110        -536.3293041 0.53739        -536.8666959  20.211  13.436   2.695  39.697
   5     -536.8666959 0.10530E-01    -536.8561663 0.85234        -537.7085083   5.038   4.871   4.701  22.761

 Number of TS in the path       =      7
 Number of cycles               =      6

 Elapsed time=                                96.36
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             23059 time=          46.50 %= 48.3
 OPTIM> # of energy+gradient+Hessian calls=       520 time=          28.16 %= 29.2
