
 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 05/23/2012 at 21:11:33
  [-O]verwriting output

File Assignments:
|  MDIN: min.in                                                                
| MDOUT: min.out                                                               
|INPCRD: coords.inpcrd                                                         
|  PARM: coords.prmtop                                                         
|RESTRT: coords.rst                                                            
|  REFC: refc                                                                  
| MDVEL: mdvel                                                                 
|  MDEN: mden                                                                  
| MDCRD: coords.mdcrd                                                          
|MDINFO: mdinfo                                                                
|INPDIP: inpdip                                                                
|RSTDIP: rstdip                                                                


 Here is the input file:

Minimization                                                                   
&cntrl                                                                         
   imin=1, maxcyc=1, ncyc=1,                                                   
   igb=2, saltcon=0.2,                                                         
   ntpr=1, ntx=1, ntb=0,                                                       
   cut = 999.0                                                                 
 /                                                                             
	                                                                              

--------------------------------------------------------------------------------
   1.  RESOURCE   USE: 
--------------------------------------------------------------------------------

| Flags:                                                                        
| New format PARM file being parsed.
| Version =    1.000 Date = 02/24/09 Time = 08:52:47
 NATOM  =     218 NTYPES =      12 NBONH =     102 MBONA  =     123
 NTHETH =     230 MTHETA =     169 NPHIH =     463 MPHIA  =     323
 NHPARM =       0 NPARM  =       0 NNB   =    1202 NRES   =      12
 NBONA  =     123 NTHETA =     169 NPHIA =     323 NUMBND =      27
 NUMANG =      57 NPTRA  =      40 NATYP =      21 NPHB   =       0
 IFBOX  =       0 NMXRS  =      24 IFCAP =       0 NEXTRA =       0
 NCOPY  =       0

 Implicit solvent radii are modified Bondi radii (mbondi)                                                   

|     Memory Use     Allocated
|     Real               14260
|     Hollerith           1322
|     Integer            31189
|     Max Pairs              1
|     nblistReal             0
|     nblist Int             0
|       Total              238 kbytes
| Duplicated    0 dihedrals
| Duplicated    0 dihedrals

--------------------------------------------------------------------------------
   2.  CONTROL  DATA  FOR  THE  RUN
--------------------------------------------------------------------------------

                                                                                

General flags:
     imin    =       1, nmropt  =       0
     ifswitch=       0, fswitchbeta=  10.000
 mdread> no continuous cutoff will be used for non-bonded terms

Nature and format of input:
     ntx     =       1, irest   =       0, ntrx    =       1

Nature and format of output:
     ntxo    =       1, ntpr    =       1, ntrx    =       1, ntwr    =     500
     iwrap   =       0, ntwx    =       0, ntwv    =       0, ntwe    =       0
     ioutfm  =       0, ntwprt  =       0, idecomp =       0, rbornstat=      0

Potential function:
     ntf     =       1, ntb     =       0, igb     =       2, nsnb    =      25
     ipol    =       0, gbsa    =       0, iesp    =       0
     dielc   =   1.00000, cut     = 999.00000, intdiel =   1.00000
     saltcon =   0.20000, offset  =   0.09000, gbalpha=    0.80000
     gbbeta  =   0.00000, gbgamma =   2.90912, surften =   0.00500
     rdt     =   0.00000, rgbmax  =  25.00000
     alpb  =        0
     scnb    =   2.00000, scee    =   1.20000

Frozen or restrained atoms:
     ibelly  =       0, ntr     =       0

Energy minimization:
     maxcyc  =       1, ncyc    =       1, ntmin   =       1
     dx0     =   0.01000, drms    =   0.00010
|  INFO: Old style inpcrd file read


--------------------------------------------------------------------------------
   3.  ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

                                                                                
 begin time read from input coords =     0.000 ps

 Number of triangulated 3-point waters found:        0
 getparams> Number of atoms (or variables)  determined as    218
 keyword> Local permutational alignment: alignment threshold=        1.00000
 keyword> Local permutational alignment: alignment cutoff=           5.00000
 keyword> Number of groups of permutable atoms=    25
read argument: coords.prmtop 
Reading parm file (coords.prmtop)
title:
                                                                                
 fetchz> Hybrid EF/BFGS transition state search, maximum steps= 250
         maximum tangent space steps=   5 or  100 when overlap is better than     0.999900
 fetchz> Uphill mode is    0 for initial step and    0 after that
 fetchz> Steps for largest Hessian e/vector= 100, smallest e/vector=2000 convergence at       0.0020%

 fetchz>  654 Cartesian coordinates will be optimised for  218 AMBER atoms

 fetchz> Lowest   1 eigenvalues and eigenvectors will be calculated non-iteratively
 fetchz> Point group checked when RMS force <     0.00100000, highest symmetry axis tested for=  6
 fetchz> Initial distance and eigenvalue tolerances in symmetry determination=     0.00010000     0.00010000
 fetchz> Minimum number of optimization steps=     0
 keywords> Cutoff for identifying atoms in the same orbit=    0.2000000000    
 keywords> lpermdist neighbours, threshold, max sep=    10     1.000000000         3
 fetchz> Convergence criterion for LBFGS optimization: RMS force< 0.10000000E-05 maximum steps= 10000
 fetchz> Maximum energy rise in LBFGS minimization=    0.1000000000E-01
 fetchz> Number of updates in LBFGS=    10000
 fetchz> Number of updates in XLBFGS=   4
 fetchz> Number of updates in mind=   4
 fetchz> Initial guess for diagonal elements in LBFGS=     0.0100
 fetchz> Initial guess for diagonal elements in XLBFGS=    0.1000
 fetchz> Maximum step size in LBFGS energy minimization=     0.1000
 fetchz> Maximum step size in XLBFGS=    0.2000
 fetchz> Maximum step size in LBFGS neb image minimization=                 0.2000
 fetchz> Warnings will be issued if atoms become closer than 0.5 units
 fetchz> Coordinates for intermediate steps will not be dumped to file points


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -456.3232521     RMS force=    0.9228759325E-06
 OPTIM> Final energy  =    -453.4164964     RMS force=    0.8854358076E-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=     51838.    
 decide> The unconnected minima in the chain and their distances are:
     2       37.29     1 
 

 tryconnect> 385-iteration DNEB run for minima 1_S and 2_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0296 Dev= 0.55% S= 40.63 time= 31.62
 Following    2 images are candidates for TS:    6    8  
 Converged to TS (number of iterations):        126
 Converged to TS (number of iterations):        102
 DNEB run yielded 2 true transition state(s) time= 124.34

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1316 steps. Energy=    -455.5998591       time=      14.70
 Minus side of path:                    1240 steps. Energy=    -454.2821879       time=      13.36

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.5998591  1.4214         -454.1784179 0.10377         -454.2821879  26.390  25.881   5.295  41.175
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1356 steps. Energy=    -455.5998591       time=      15.08
 Minus side of path:                    1253 steps. Energy=    -455.0287733       time=      13.67

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.5998591  1.9717         -453.6282052  1.4006         -455.0287733  28.423  22.319   8.484  25.694
        Known (#3)                                              *NEW* (Placed in 5)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     15235.    
 decide> The unconnected minima in the chain and their distances are:
     2       23.14     4     3       14.16     1 
 

 tryconnect> 210-iteration DNEB run for minima 2_F and 4_U using 6 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.288396211    
 Double-ended search iterations= 210 RMS= 0.1006 Dev= 0.06% S= 24.05 time= 9.46
 Following    1 images are candidates for TS:    3  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 144.55

 tryconnect> 140-iteration DNEB run for minima 1_S and 3_U using 4 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.550936371    
 Double-ended search iterations= 140 RMS= 0.0508 Dev= 0.12% S= 14.28 time= 4.37
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         90
 DNEB run yielded 1 true transition state(s) time=  57.58

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1380 steps. Energy=    -457.3737179       time=      19.78
 Minus side of path:                    1236 steps. Energy=    -455.5998591       time=      14.83

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -457.3737179  2.3139         -455.0598524 0.54001         -455.5998591  36.226  31.923   1.682 129.578
        *NEW* (Placed in 6)                                     Known (#3)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      2 missing connections, weight=     23227.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.99     5     3       14.16     1 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 5_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 1.7437 Dev= 0.17% S= 26.86 time= 12.84
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         37
 DNEB run yielded 1 true transition state(s) time=  31.19

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1239 steps. Energy=    -453.4164964       time=      14.74
 Minus side of path:                    1286 steps. Energy=    -455.0287733       time=      15.50

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -453.4164964 0.17904         -453.2374556  1.7913         -455.0287733  26.786  25.995   4.883  44.642
        Known (#2)                                              Known (#5)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 805-iteration DNEB run for minima 1_S and 3_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.957339570    
 Double-ended search iterations= 805 RMS= 0.0406 Dev= 3.56% S= 15.13 time= 139.17
 Following    1 images are candidates for TS:   19  
 Converged to TS (number of iterations):        141
 DNEB run yielded 1 true transition state(s) time=  77.41
 isnewts> transition state is the same as number        3 energy=     -455.0598524223
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 5 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1390 steps. Energy=    -457.3737179       time=      18.91
 Minus side of path:                    1242 steps. Energy=    -455.5998591       time=      15.14

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -457.3737179  2.3139         -455.0598524 0.54001         -455.5998591  36.225  31.924   1.682 129.576
        Known (#6)                                              Known (#3)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     19364.    
 decide> The unconnected minima in the chain and their distances are:
     4       26.85     1 
 

 tryconnect> 280-iteration DNEB run for minima 1_S and 4_F using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0780 Dev= 0.22% S= 28.05 time= 16.86
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         81
 DNEB run yielded 1 true transition state(s) time=  49.98

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1186 steps. Energy=    -454.2736721       time=      12.90
 Minus side of path:                    1280 steps. Energy=    -455.1909320       time=      14.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -454.2736721 0.11606E-01     -454.2620664 0.92887         -455.1909320  12.451  12.296   2.829  77.055
        *NEW* (Placed in 7)                                     *NEW* (Placed in 8)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 8 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     16421.    
 decide> The unconnected minima in the chain and their distances are:
     4        5.54     7     7       25.33     1 
 

 tryconnect> 70-iteration DNEB run for minima 4_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2066 Dev= 0.03% S= 5.58 time= 1.08
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         78
 DNEB run yielded 1 true transition state(s) time=  46.53
 isnewts> transition state is the same as number        6 energy=     -454.2620664328
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 7 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1301 steps. Energy=    -455.1909320       time=      15.43
 Minus side of path:                    1203 steps. Energy=    -454.2736721       time=      15.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.1909320 0.92887         -454.2620664 0.11606E-01     -454.2736721  12.451  12.296   2.828  77.092
        Known (#8)                                              Known (#7)
 Connection established between members of the U set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 7_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0542 Dev= 0.17% S= 26.09 time= 13.04
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        114
 DNEB run yielded 1 true transition state(s) time=  68.39

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1229 steps. Energy=    -456.3232520       time=      13.37
 Minus side of path:                    1237 steps. Energy=    -455.5882836       time=      12.78

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -456.3232520 0.78342         -455.5398322 0.48451E-01     -455.5882836  13.233  13.069   2.187  99.683
        Known (#1)                                              *NEW* (Placed in 9)
 Unconnected minimum 9 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 9 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     258.37    
 decide> The unconnected minima in the chain and their distances are:
     3        6.37     9 
 

 tryconnect> 70-iteration DNEB run for minima 3_F and 9_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.0589 Dev= 0.01% S= 6.40 time= 1.06
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         29
 DNEB run yielded 1 true transition state(s) time=  24.95

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1208 steps. Energy=    -455.5998591       time=      12.45
 Minus side of path:                    1239 steps. Energy=    -455.5882836       time=      12.95

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -455.5998591 0.33831         -455.2615489 0.32673         -455.5882836   6.907   6.369   3.236  67.367
        Known (#3)                                              Known (#9)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -456.3232521 0.78342        -455.5398322 0.48451E-01    -455.5882836  13.233  13.069   2.187  99.683
   9     -455.5882836 0.32673        -455.2615489 0.33831        -455.5998591   6.907   6.369   3.236  67.367
   2     -455.5998591  1.9717        -453.6282052  1.4006        -455.0287733  28.423  22.319   8.484  25.694
   4     -455.0287733  1.7913        -453.2374556 0.17904        -453.4164964  26.786  25.995   4.883  44.642

 Number of TS in the path       =      4
 Number of cycles               =      6

 Elapsed time=                              1120.78
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             66194 time=         502.70 %= 44.9
 OPTIM> # of energy+gradient+Hessian calls=      1048 time=         317.11 %= 28.3
