
 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 21:31:15
  [-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


 KeyInt>> Using natural internal coordinates. # of coords =        648
 KeyInt>> Parameter file for internal coordinates is naturals-noH.par                                                                                    
 KeyInt>> KD, NNZ are         74      7440
 KeyInt>> Back transform convergence (for interpolation)     0.1000000000E-07
 KeyInt>> Back transform convergence criterion (except for interpolation)     0.1000000000E-03
 KeyInt>> Using internal coordinates for interpolation.
 KeyInt>> Permuting endpoint atoms to minimise torsion distance
 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -446.0744355     RMS force=    0.9388488662E-06
 OPTIM> Final energy  =    -444.2246350     RMS force=    0.8581405056E-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=     17107.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.77     1 
 

 tryconnect> 245-iteration DNEB run for minima 1_S and 2_F using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.0561 Dev= 0.44% S= 26.87 time= 13.23
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=  42.00

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1389 steps. Energy=    -446.6349032       time=      17.94
 Minus side of path:                    1885 steps. Energy=    -447.3016277       time=      32.49

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.6349032  3.1682         -443.4667316  3.8349         -447.3016277  50.520  34.753   3.096  70.411
        *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      1 steps with      1 missing connections, weight=     34214.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.77     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 805 RMS= 0.0261 Dev= 4.72% S= 28.97 time= 141.38
 Following    1 images are candidates for TS:   13  
 Converged to TS (number of iterations):         38
 DNEB run yielded 1 true transition state(s) time=  36.56
 isnewts> transition state is the same as number        1 energy=     -443.4667316406
 tryconnect> Try the path again for ts      1 with pushoff=    0.1000000000E-01

 >>>>>  Path run for ts 2 ...
 tryconnect> Trying this transition state path again with pushoff=    0.1000000000E-01
 Plus  side of path:                    1396 steps. Energy=    -446.6349032       time=      17.19
 Minus side of path:                    1875 steps. Energy=    -447.3016277       time=      26.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.6349032  3.1682         -443.4667316  3.8349         -447.3016277  50.505  34.730   3.106  70.180
        Known (#3)                                              Known (#4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     39559.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.49     3     3       26.58     1 
 

 tryconnect> 280-iteration DNEB run for minima 2_F and 3_U using 8 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.6507276371    
 Double-ended search iterations= 280 RMS= 0.0485 Dev= 0.32% S= 28.91 time= 17.23
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         72
 DNEB run yielded 1 true transition state(s) time=  48.57

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1334 steps. Energy=    -444.9554786       time=      16.06
 Minus side of path:                    1320 steps. Energy=    -444.2246350       time=      16.69

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.9554786 0.73438         -444.2210965 0.35385E-02     -444.2246350  18.631  18.304   5.204  41.892
        *NEW* (Placed in 5)                                     Known (#2)
 Unconnected minimum 5 found its way to F set.

 tryconnect> 245-iteration DNEB run for minima 1_S and 3_U using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 245 RMS= 0.1215 Dev= 1.73% S= 30.46 time= 12.94
 Following    2 images are candidates for TS:    3    6  
 Converged to TS (number of iterations):         63
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 1 true transition state(s) time= 188.56
 isnewts> transition state is the same as number        1 energy=     -443.4667316407
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     67456.    
 decide> The unconnected minima in the chain and their distances are:
     5       40.71     1 
 

 tryconnect> 420-iteration DNEB run for minima 1_S and 5_F using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0664 Dev= 2.53% S= 46.40 time= 38.12
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         49
 DNEB run yielded 1 true transition state(s) time=  38.85
 isnewts> transition state is the same as number        1 energy=     -443.4667316421
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     79118.    
 decide> The unconnected minima in the chain and their distances are:
     2       27.49     3     3       26.58     1 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 3_U using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.2839103126    
 Double-ended search iterations= 805 RMS= 0.0184 Dev= 8.89% S= 36.48 time= 139.81
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         19
 DNEB run yielded 1 true transition state(s) time=  24.36
 isnewts> transition state is the same as number        3 energy=     -444.2210965344
 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:                    1368 steps. Energy=    -444.9554786       time=      17.42
 Minus side of path:                    1298 steps. Energy=    -444.2246350       time=      16.02

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.9554786 0.73438         -444.2210965 0.35385E-02     -444.2246350  18.632  18.305   5.202  41.911
        Known (#5)                                              Known (#2)
 Alternative path found between members of the F set.

 tryconnect> 805-iteration DNEB run for minima 1_S and 3_U using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      1.352816022    
 Double-ended search iterations= 805 RMS= 0.0647 Dev= 6.01% S= 38.83 time= 138.90
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         25
 DNEB run yielded 1 true transition state(s) time=  26.79
 isnewts> transition state is the same as number        1 energy=     -443.4667316406
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 5 minima and 4 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=     96517.    
 decide> The unconnected minima in the chain and their distances are:
     2       36.28     4     4       36.53     1 
 

 tryconnect> 350-iteration DNEB run for minima 2_F and 4_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0573 Dev= 1.69% S= 39.54 time= 26.60
 Following    1 images are candidates for TS:    4  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=  39.28
 isnewts> transition state is the same as number        1 energy=     -443.4667316406
 tryconnect> Will not repeat search for TS      1 same as TS      1

 tryconnect> 350-iteration DNEB run for minima 1_S and 4_U using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.1064 Dev= 0.42% S= 39.07 time= 26.74
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):        108
 DNEB run yielded 1 true transition state(s) time=  70.98

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1501 steps. Energy=    -446.0744355       time=      21.89
 Minus side of path:                    1357 steps. Energy=    -446.6425488       time=      18.06

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.0744355 0.44187         -445.6325693  1.0100         -446.6425488  33.476  28.321   2.472  88.175
        Known (#1)                                              *NEW* (Placed in 6)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     17173.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.80     6 
 

 tryconnect> 245-iteration DNEB run for minima 2_F and 6_S using 7 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.9156391332    
 Double-ended search iterations= 245 RMS= 0.4394 Dev= 0.73% S= 27.06 time= 13.07
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         43
 DNEB run yielded 1 true transition state(s) time=  39.36
 isnewts> transition state is the same as number        1 energy=     -443.4667316406
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     34347.    
 decide> The unconnected minima in the chain and their distances are:
     2       25.80     6 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 6_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant     0.6197406068    
 Double-ended search iterations= 805 RMS= 0.0203 Dev= 6.97% S= 32.08 time= 140.59
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         27
 DNEB run yielded 1 true transition state(s) time=  28.93
 isnewts> transition state is the same as number        1 energy=     -443.4667316406
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     37846.    
 decide> The unconnected minima in the chain and their distances are:
     5       33.57     6 
 

 tryconnect> 350-iteration DNEB run for minima 5_F and 6_S using 10 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3286616756    
 Double-ended search iterations= 350 RMS= 0.0916 Dev= 1.78% S= 37.34 time= 26.55
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         69
 DNEB run yielded 1 true transition state(s) time=  54.36
 isnewts> transition state is the same as number        1 energy=     -443.4667316250
 tryconnect> Will not repeat search for TS      1 same as TS      1
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 6 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=     66211.    
 decide> The unconnected minima in the chain and their distances are:
     5       39.16     3     4       18.31     6 
 

 tryconnect> 385-iteration DNEB run for minima 3_U and 5_F using 11 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.2335737168    
 Double-ended search iterations= 385 RMS= 0.0412 Dev= 1.06% S= 42.48 time= 32.10
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=  45.73

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1422 steps. Energy=    -446.6349032       time=      18.38
 Minus side of path:                    1312 steps. Energy=    -444.9554786       time=      17.44

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.6349032  2.0109         -444.6239737 0.33150         -444.9554786  42.229  39.428   5.651  38.576
        Known (#3)                                              Known (#5)
 Unconnected minimum 3 found its way to F set.

 tryconnect> 175-iteration DNEB run for minima 4_F and 6_S using 5 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      1.812902854    
 Double-ended search iterations= 175 RMS= 0.0698 Dev= 0.04% S= 18.48 time= 6.97
 Following    1 images are candidates for TS:    5  
 Converged to TS (number of iterations):         50
 DNEB run yielded 1 true transition state(s) time=  41.64

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1375 steps. Energy=    -447.3016277       time=      19.51
 Minus side of path:                    1299 steps. Energy=    -446.6425488       time=      19.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.3016277 0.66281         -446.6388217 0.37271E-02     -446.6425488  18.626  18.315   3.130  69.651
        Known (#4)                                              Known (#6)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   5     -446.0744355 0.44187        -445.6325693  1.0100        -446.6425488  33.476  28.321   2.472  88.175
   7     -446.6425488 0.37271E-02    -446.6388217 0.66281        -447.3016277  18.626  18.315   3.130  69.651
   1     -447.3016277  3.8349        -443.4667316  3.1682        -446.6349032  50.520  34.753   3.096  70.411
   6     -446.6349032  2.0109        -444.6239737 0.33150        -444.9554786  42.229  39.428   5.651  38.576
   3     -444.9554786 0.73438        -444.2210965 0.35385E-02    -444.2246350  18.631  18.304   5.204  41.892

 Number of TS in the path       =      5
 Number of cycles               =     10

 Elapsed time=                              1774.95
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            143303 time=        1082.13 %= 61.0
 OPTIM> # of energy+gradient+Hessian calls=       986 time=         301.93 %= 17.0
