
 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 05/27/2012 at 22:14:05
  [-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> Constraint potential parameters read from file congeom.dat
 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
 fetchz> Using constraint potential for initial interpolation in each cycle
         with absolute distance change tolerance         0.30000
         extra distance before turning on constraint potential         0.17500
         constraint spring constant=       10.00000
         image distance spring constant=        1.00000
         repulsion factor between unconstrained atoms=      100.00000
         repulsion cutoff will be the minimum of         1.55000 and the shortest distance in the end points
         fraction for restoring true potential=        0.99000
         maximum separation of atoms in sequence for constraint=   218
         minimum separation of atoms in sequence for repulsion=     0
         maximum optimization steps for constrained potential=  300001
         initial # images for constrained potential, maximum, check interval=       3      75      25
         number of interpolation attempts and initial image increment=       2      12
         RMS gradient per image tolerance for constrained potential=        0.01000
         maximum optimization steps for constrained/real potential=      25
         maximum steps for relaxation after adding a new atom before backtrack=     200
         maximum number of constraints per atom=     6
         maximum energy per image for convergence during constraint potential phase=        0.1000000000
         interval for checking repulsive interactions=    10
         multiple of cutoff for repulsion neighbour list=        2.0000000000
         adding terms for constraint internal minima
         Minimum and Maximum image separations:         0.10000       10.00000
 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> Number of updates in qci=   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=    -443.3554718     RMS force=    0.9480096869E-06
 OPTIM> Final energy  =    -441.2242490     RMS force=    0.9686019757E-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 from interp function and dist, power=     3

 checkperc> Increasing con cutoff atoms   142  143 from     0.23123E-02 to     0.23387E-02 ref=     1.0826    
 checkperc> Increasing con cutoff atoms   171  173 from     0.82345E-02 to     0.10607E-01 ref=     3.1361    
 checkperc> Increasing con cutoff atoms   172  176 from     0.36193E-01 to     0.37412E-01 ref=     2.4570    
 checkperc> Increasing con cutoff atoms   174  194 from     0.63182E-02 to     0.92143E-02 ref=     1.5453    
 checkperc> Increasing con cutoff atoms   195  196 from     0.14110E-01 to     0.15739E-01 ref=     2.2669    
 checkperc> Increasing con cutoff atoms   195  197 from     0.67694E-02 to     0.17784E-01 ref=     3.1381    
 checkperc> Increasing con cutoff atoms   196  197 from     0.11629E-02 to     0.35058E-02 ref=     1.0116    
 checkperc> Increasing con cutoff atoms   196  198 from     0.38283E-02 to     0.42405E-02 ref=     1.4779    
 checkperc> Increasing con cutoff atoms   196  200 from     0.30611E-01 to     0.48662E-01 ref=     2.4860    
 checkperc> Increasing con cutoff atoms   198  200 from     0.37218E-02 to     0.41737E-02 ref=     1.5442    
 checkperc> Increasing con cutoff atoms   199  216 from     0.13209E-01 to     0.14812E-01 ref=     2.1136    
 checkperc> Increasing con cutoff atoms   199  218 from     0.13353     to     0.13438     ref=     3.1268    
 checkperc> Increasing con cutoff atoms   200  202 from     0.79979E-03 to     0.82701E-03 ref=     1.0910    
 checkperc> Increasing con cutoff atoms   201  202 from     0.18656E-01 to     0.19065E-01 ref=     1.7576    
 checkperc> Increasing con cutoff atoms   203  207 from     0.23702E-01 to     0.24326E-01 ref=     2.1543    
 checkperc> Increasing con cutoff atoms   206  210 from     0.10339E-01 to     0.12598E-01 ref=     2.1538    
 checkperc> Increasing con cutoff atoms   206  211 from     0.90916E-02 to     0.11135E-01 ref=     2.1519    
 checkperc> Increasing con cutoff atoms   207  208 from     0.12833E-01 to     0.13199E-01 ref=     1.7675    
 checkperc> Increasing con cutoff atoms   209  212 from     0.30877E-02 to     0.42833E-02 ref=     1.4892    
 checkperc> Increasing con cutoff atoms   209  215 from     0.10502E-01 to     0.14476E-01 ref=     2.0882    
 checkperc> Increasing con cutoff atoms   211  212 from     0.13563E-01 to     0.17994E-01 ref=     2.1268    
 checkperc> Increasing con cutoff atoms   213  214 from     0.68872E-02 to     0.84728E-02 ref=     1.6336    
 initialise> Interpolation metric value for minima 1 and 2 is      30.35394324    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     28025.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.34     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 3 initial images  (interp attempt #1)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    57
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    220 fraction=    0.990000 images=     3 time=       0.6
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    245 steps, energy/image=    -278.6613189     RMS=18.29435940     images=   4
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   38.23     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0286 Dev= 0.88% S= 32.09 time= 32.09
 Following    1 images are candidates for TS:   10  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 124.52
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     56050.    
 decide> The unconnected minima in the chain and their distances are:
     2       30.34     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    57
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    170 fraction=    0.990000 images=    15 time=       1.9
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    195 steps, energy/image=    -408.4967893     RMS=8.647010685     images=  16
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   45.27     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 805 RMS= 0.0249 Dev= 5.71% S= 39.46 time= 139.41
 Following    1 images are candidates for TS:   22  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 117.45
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> There appear to be no connections left to try in DIJKSTRA
 decide> Increasing maximum number of images to     25 and clearing weights
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     2006.0    
 decide> The unconnected minima in the chain and their distances are:
     2       10.00     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    57
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    164 fraction=    0.990000 images=    15 time=       2.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    189 steps, energy/image=    -423.4902387     RMS=10.11148164     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   39.79     Attempts, images and iterations=     3    25   875
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 875 RMS= 0.0288 Dev= 5.34% S= 39.15 time= 164.10
 Following    1 images are candidates for TS:   24  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 117.71
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> There appear to be no connections left to try in DIJKSTRA
 decide> Increasing maximum number of images to     27 and clearing weights
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     2006.0    
 decide> The unconnected minima in the chain and their distances are:
     2       10.00     1 
 

 tryconnect> Interpolation for minima 1_S and 2_F using 15 initial images  (interp attempt #2)  ...
 intlbfgs> Maximum number of steps for constraint potential phase is 300001
 intlbfgs> Total number of atoms moving less than threshold=    57
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    163 fraction=    0.990000 images=    15 time=       2.0
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    188 steps, energy/image=    -426.6441779     RMS=6.654289535     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   40.08     Attempts, images and iterations=     3    27   945
 lbfgs> Final DNEB force constant     0.3804669723    
 Double-ended search iterations= 945 RMS= 0.0211 Dev= 5.82% S= 39.53 time= 191.36
 Following    2 images are candidates for TS:    5   26  
 Converged to TS (number of iterations):         31
 Converged to TS (number of iterations):         21
 DNEB run yielded 2 true transition state(s) time=  48.59

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1265 steps. Energy=    -443.3920258       time=      13.02
 Minus side of path:                    1295 steps. Energy=    -443.3554718       time=      13.45

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -443.3920258 0.86647E-01     -443.3053788 0.50093E-01     -443.3554718   3.267   2.704   7.840  27.805
        *NEW* (Placed in 3)                                     Known (#1)
 checkperc> Increasing con cutoff atoms   160  174 from     0.27310E-01 to     0.29260E-01 ref=     3.8522    
 checkperc> Increasing con cutoff atoms   171  173 from     0.10607E-01 to     0.13108E-01 ref=     3.1361    
 checkperc> Increasing con cutoff atoms   174  194 from     0.92143E-02 to     0.92161E-02 ref=     1.5453    
 checkperc> Increasing con cutoff atoms   174  195 from     0.13287E-01 to     0.24343E-01 ref=     2.4202    
 checkperc> Increasing con cutoff atoms   176  194 from     0.35448E-01 to     0.37906E-01 ref=     2.5606    
 checkperc> Increasing con cutoff atoms   195  196 from     0.15739E-01 to     0.19065E-01 ref=     2.2669    
 checkperc> Increasing con cutoff atoms   195  197 from     0.17784E-01 to     0.18323E-01 ref=     3.1381    
 checkperc> Increasing con cutoff atoms   196  198 from     0.42405E-02 to     0.58253E-02 ref=     1.4779    
 checkperc> Increasing con cutoff atoms   196  200 from     0.48662E-01 to     0.50716E-01 ref=     2.4860    
 checkperc> Increasing con cutoff atoms   198  200 from     0.41737E-02 to     0.46919E-02 ref=     1.5442    
 checkperc> Increasing con cutoff atoms   200  202 from     0.82701E-03 to     0.83619E-03 ref=     1.0910    
 checkperc> Increasing con cutoff atoms   203  207 from     0.24326E-01 to     0.26554E-01 ref=     2.1543    
 checkperc> Increasing con cutoff atoms   206  210 from     0.12598E-01 to     0.15920E-01 ref=     2.1538    
 checkperc> Increasing con cutoff atoms   206  211 from     0.11135E-01 to     0.12276E-01 ref=     2.1519    
 checkperc> Increasing con cutoff atoms   206  215 from     0.89239E-01 to     0.95732E-01 ref=     2.7749    
 checkperc> Increasing con cutoff atoms   207  208 from     0.13199E-01 to     0.14044E-01 ref=     1.7675    
 checkperc> Increasing con cutoff atoms   209  215 from     0.14476E-01 to     0.16512E-01 ref=     2.0882    
 checkperc> Increasing con cutoff atoms   210  212 from     0.12522E-01 to     0.13527E-01 ref=     2.1272    
 checkperc> Increasing con cutoff atoms   210  214 from     0.64106E-01 to     0.65087E-01 ref=     2.4271    
 checkperc> Increasing con cutoff atoms   211  214 from     0.55771E-01 to     0.62905E-01 ref=     2.4246    
 Unconnected minimum 3 found its way to S set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1842 steps. Energy=    -443.3554718       time=      22.69
 Minus side of path:                    1301 steps. Energy=    -441.2242490       time=      13.60

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -443.3554718  2.6506         -440.7048934 0.51936         -441.2242490  31.974  30.353   2.541  85.809
        Known (#1)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   2     -443.3554718  2.6506        -440.7048934 0.51936        -441.2242490  31.974  30.353   2.541  85.809

 Number of TS in the path       =      1
 Number of cycles               =      4

 Elapsed time=                              1015.00
 OPTIM> # of energy calls=                          8 time=           0.06 %=  0.0
 OPTIM> # of energy+gradient calls=             84317 time=         626.61 %= 61.7
 OPTIM> # of energy+gradient+Hessian calls=       802 time=         225.59 %= 22.2
