
 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 22:11:09
  [-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=    -451.9766922     RMS force=    0.9939492980E-06
 OPTIM> Final energy  =    -450.7070847     RMS force=    0.8512420260E-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

 initialise> Interpolation metric value for minima 1 and 2 is      473.4742364    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     25131.    
 decide> The unconnected minima in the chain and their distances are:
     2       28.82     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=    72
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    314 fraction=    0.990000 images=     4 time=       0.7
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    339 steps, energy/image=    -425.1494139     RMS=.8699415140     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   39.76     Attempts, images and iterations=     0    11   385
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0927 Dev= 1.87% S= 43.58 time= 31.76
 Following    3 images are candidates for TS:    3    6    9  
 Converged to TS (number of iterations):         92
 Converged to TS (number of iterations):         60
 Converged to TS (number of iterations):         47
 DNEB run yielded 3 true transition state(s) time= 132.63

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1322 steps. Energy=    -451.2652397       time=      15.15
 Minus side of path:                    1326 steps. Energy=    -450.7792103       time=      14.25

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.2652397 0.99616         -450.2690773 0.51013         -450.7792103  25.310  23.700   1.767 123.386
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 checkperc> Increasing con cutoff atoms   160  173 from     0.46000E-01 to     0.48399E-01 ref=     2.5620    
 checkperc> Increasing con cutoff atoms   172  174 from     0.54629E-02 to     0.57768E-02 ref=     1.4700    
 checkperc> Increasing con cutoff atoms   107  113 from     0.50339E-01 to     0.50670E-01 ref=     2.5548    
 checkperc> Increasing con cutoff atoms   109  110 from     0.14083E-01 to     0.14217E-01 ref=     2.1318    
 checkperc> Increasing con cutoff atoms   160  173 from     0.48399E-01 to     0.53602E-01 ref=     2.5620    
 checkperc> Increasing con cutoff atoms   174  176 from     0.66696E-02 to     0.77825E-02 ref=     1.5376    
 checkperc> Increasing con cutoff atoms   176  180 from     0.24125E-01 to     0.28316E-01 ref=     2.5370    
 checkperc> Increasing con cutoff atoms   176  181 from     0.47769E-01 to     0.53441E-01 ref=     2.8612    
 checkperc> Increasing con cutoff atoms   176  182 from     0.10939E-01 to     0.13242E-01 ref=     3.6934    
 checkperc> Increasing con cutoff atoms   176  183 from     0.17925E-01 to     0.20064E-01 ref=     4.6005    
 checkperc> Increasing con cutoff atoms   176  189 from     0.56423E-01 to     0.62621E-01 ref=     4.8302    
 checkperc> Increasing con cutoff atoms   176  190 from     0.63523E-01 to     0.70996E-01 ref=     5.5562    
 checkperc> Increasing con cutoff atoms   176  191 from     0.59406E-01 to     0.66319E-01 ref=     3.4401    
 checkperc> Increasing con cutoff atoms   176  192 from     0.80497E-01 to     0.89682E-01 ref=     3.2690    
 checkperc> Increasing con cutoff atoms   179  180 from     0.23245E-02 to     0.25674E-02 ref=     1.3524    
 checkperc> Increasing con cutoff atoms   179  181 from     0.64355E-02 to     0.70615E-02 ref=     2.1638    
 checkperc> Increasing con cutoff atoms   179  186 from     0.40232E-02 to     0.41848E-02 ref=     4.5043    
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1309 steps. Energy=    -451.5626961       time=      14.43
 Minus side of path:                    1341 steps. Energy=    -451.2652397       time=      14.37

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.5626961  3.5549         -448.0078258  3.2574         -451.2652397  27.410  20.934  19.435  11.217
        *NEW* (Placed in 5)                                     Known (#3)
 checkperc> Increasing con cutoff atoms   196  197 from     0.14680E-02 to     0.19128E-02 ref=     1.0110    
 Connection established between members of the U set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1333 steps. Energy=    -451.5626961       time=      14.36
 Minus side of path:                    1316 steps. Energy=    -450.7070847       time=      14.27

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.5626961  3.9916         -447.5711144  3.1360         -450.7070847   9.223   7.381  27.775   7.849
        Known (#5)                                              Known (#2)
 Unconnected minimum 5 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     3506.9    
 decide> The unconnected minima in the chain and their distances are:
     4       15.18     1 
 

 tryconnect> Interpolation for minima 1_S and 4_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=   187
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step     99 fraction=    0.990000 images=     3 time=       0.1
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    124 steps, energy/image=    -266.7101747     RMS=23.93129408     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   25.07     Attempts, images and iterations=     0     7   245
 lbfgs> Final DNEB force constant      1.998725396    
 Double-ended search iterations= 245 RMS= 0.2740 Dev= 0.51% S= 17.22 time= 12.74
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):        102
 DNEB run yielded 1 true transition state(s) time=  58.20
 isnewts> transition state is the same as number        1 energy=     -450.2690772514
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 4 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1321 steps. Energy=    -451.2652397       time=      14.58
 Minus side of path:                    1320 steps. Energy=    -450.7792103       time=      14.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.2652397 0.99616         -450.2690773 0.51013         -450.7792103  25.310  23.700   1.767 123.384
        Known (#3)                                              Known (#4)
 Alternative path found between members of the F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     7013.8    
 decide> The unconnected minima in the chain and their distances are:
     4       15.18     1 
 

 tryconnect> Interpolation for minima 1_S and 4_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=   187
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    144 fraction=    0.990000 images=    15 time=       0.2
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    169 steps, energy/image=    -442.1958039     RMS=1.291564518     images=  15
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      4
 intlbfgs> DNEB for minima      1     4 dist=   23.69     Attempts, images and iterations=     3    23   805
 lbfgs> Final DNEB force constant     0.1300625854    
 Double-ended search iterations= 805 RMS= 0.0211 Dev= 4.19% S= 27.65 time= 136.99
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         89
 DNEB run yielded 1 true transition state(s) time=  51.51
 isnewts> transition state is the same as number        1 energy=     -450.2690772492
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     17195.    
 decide> The unconnected minima in the chain and their distances are:
     3       25.78     1 
 

 tryconnect> Interpolation for minima 1_S and 3_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=    47
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    210 fraction=    0.990000 images=     3 time=       0.7
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    235 steps, energy/image=    -352.6019673     RMS=9.841262595     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      3
 intlbfgs> DNEB for minima      1     3 dist=   29.47     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.7909635100    
 Double-ended search iterations= 280 RMS= 0.0759 Dev= 1.74% S= 27.94 time= 16.60
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         60
 DNEB run yielded 1 true transition state(s) time=  37.43

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1293 steps. Energy=    -451.2652397       time=      13.24
 Minus side of path:                    1319 steps. Energy=    -452.0033254       time=      13.64

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -451.2652397 0.31211         -450.9531295  1.0502         -452.0033254  17.454  12.747   7.383  29.525
        Known (#3)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to F set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     12637.    
 decide> The unconnected minima in the chain and their distances are:
     6       23.27     1 
 

 tryconnect> Interpolation for minima 1_S and 6_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=    56
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    163 fraction=    0.990000 images=     3 time=       0.6
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    188 steps, energy/image=    -415.5300793     RMS=8.419560182     images=   3
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      6
 intlbfgs> DNEB for minima      1     6 dist=   27.41     Attempts, images and iterations=     0     8   280
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0109 Dev= 0.15% S= 23.39 time= 16.56
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         22
 DNEB run yielded 1 true transition state(s) time=  21.84

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1321 steps. Energy=    -452.0033254       time=      13.67
 Minus side of path:                    1292 steps. Energy=    -451.9766922       time=      13.29

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -452.0033254 0.11664         -451.8866885 0.90004E-01     -451.9766922  23.560  23.269   1.822 119.625
        Known (#6)                                              Known (#1)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   6     -451.9766922 0.90004E-01    -451.8866885 0.11664        -452.0033254  23.560  23.269   1.822 119.625
   5     -452.0033254  1.0502        -450.9531295 0.31211        -451.2652397  17.454  12.747   7.383  29.525
   2     -451.2652397  3.2574        -448.0078258  3.5549        -451.5626961  27.410  20.934  19.435  11.217
   3     -451.5626961  3.9916        -447.5711144  3.1360        -450.7070847   9.223   7.381  27.775   7.849

 Number of TS in the path       =      4
 Number of cycles               =      5

 Elapsed time=                               695.30
 OPTIM> # of energy calls=                         10 time=           0.07 %=  0.0
 OPTIM> # of energy+gradient calls=             55362 time=         405.69 %= 58.3
 OPTIM> # of energy+gradient+Hessian calls=       472 time=         130.18 %= 18.7
