
 OPTIM version 22983, Copyright (C) David J. Wales
 OPTIM comes with ABSOLUTELY NO WARRANTY; for details supply WARRANTY as an input keyword.
 This is free software, and you are welcome to redistribute it
 under certain conditions; provide keyword COPYRIGHT to see the details.

 getparams> input coordinates for AMBER9 system will be read from 
start
start               

          -------------------------------------------------------
          Amber 9  SANDER                              2006
          -------------------------------------------------------

| Run on 05/24/2012 at 18:56:04
  [-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=    -446.4477589     RMS force=    0.9934398403E-06
 OPTIM> Final energy  =    -444.8146936     RMS force=    0.9976889544E-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=     1274.3    
 decide> The unconnected minima in the chain and their distances are:
     2       10.84     1 
 

 tryconnect> 105-iteration DNEB run for minima 1_S and 2_F using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.446089162    
 Double-ended search iterations= 105 RMS= 2.5216 Dev= 2.20% S= 23.63 time= 2.69
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         41
 DNEB run yielded 1 true transition state(s) time=  31.49

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1327 steps. Energy=    -446.4477589       time=      15.38
 Minus side of path:                    1289 steps. Energy=    -444.8524861       time=      16.00

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -446.4477589  5.2767         -441.1710404  3.6814         -444.8524861  15.750  12.927   8.498  25.652
        Known (#1)                                              *NEW* (Placed in 3)
 Unconnected minimum 3 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 3 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=     1516.9    
 decide> The unconnected minima in the chain and their distances are:
     2       11.49     3 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 3_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.4720 Dev= 0.61% S= 19.75 time= 2.68
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=  32.97

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1264 steps. Energy=    -444.8524861       time=      15.14
 Minus side of path:                    1310 steps. Energy=    -442.6434194       time=      15.65

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.8524861  3.7009         -441.1515646  1.4919         -442.6434194  10.525   9.091   9.836  22.163
        Known (#3)                                              *NEW* (Placed in 4)
 Unconnected minimum 4 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 2 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     889.04    
 decide> The unconnected minima in the chain and their distances are:
     2        9.62     4 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 4_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.568374182    
 Double-ended search iterations= 70 RMS= 0.9418 Dev= 0.63% S= 13.03 time= 1.31
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         54
 DNEB run yielded 1 true transition state(s) time=  41.21

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1260 steps. Energy=    -444.5416270       time=      14.96
 Minus side of path:                    1320 steps. Energy=    -444.4784282       time=      15.59

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.5416270  2.4360         -442.1055987  2.3728         -444.4784282  14.840  10.749   8.242  26.450
        *NEW* (Placed in 5)                                     *NEW* (Placed in 6)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 6 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      2 missing connections, weight=     902.25    
 decide> The unconnected minima in the chain and their distances are:
     2        7.85     6     6        7.48     4 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1757 Dev= 0.53% S= 8.29 time= 1.31
 Following    1 images are candidates for TS:    2  
 Converged to TS (number of iterations):         45
 DNEB run yielded 1 true transition state(s) time=  33.32
 isnewts> transition state is the same as number        3 energy=     -442.1055986752
 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:                    1263 steps. Energy=    -444.5416270       time=      13.26
 Minus side of path:                    1308 steps. Energy=    -444.4784282       time=      14.12

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.5416270  2.4360         -442.1055987  2.3728         -444.4784282  14.841  10.749   8.234  26.474
        Known (#5)                                              Known (#6)
 Connection established between members of the U set.

 tryconnect> 70-iteration DNEB run for minima 4_S and 6_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.2981 Dev= 0.77% S= 9.28 time= 1.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=  25.22

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1285 steps. Energy=    -445.2288580       time=      13.57
 Minus side of path:                    1298 steps. Energy=    -442.6434194       time=      13.82

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.2288580  4.7493         -440.4795664  2.1639         -442.6434194   8.399   7.208  19.652  11.093
        *NEW* (Placed in 7)                                     Known (#4)
 Unconnected minimum 7 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     379.15    
 decide> The unconnected minima in the chain and their distances are:
     2        7.24     7 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_S using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      6.139132535    
 Double-ended search iterations= 70 RMS= 0.9160 Dev= 0.57% S= 8.57 time= 1.30
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         52
 DNEB run yielded 1 true transition state(s) time=  38.36
 isnewts> transition state is the same as number        3 energy=     -442.1055986752
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 7 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     758.30    
 decide> The unconnected minima in the chain and their distances are:
     2        7.24     7 
 

 tryconnect> 560-iteration DNEB run for minima 2_F and 7_S using 16 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      2.098661666    
 Double-ended search iterations= 560 RMS= 0.0635 Dev= 7.50% S= 14.01 time= 67.88
 Following    2 images are candidates for TS:    8   12  
 Converged to TS (number of iterations):         31
 Converged to TS (number of iterations):         47
 DNEB run yielded 2 true transition state(s) time=  65.29
 isnewts> transition state is the same as number        3 energy=     -442.1055986752
 tryconnect> Will not repeat search for TS      1 same as TS      3

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1294 steps. Energy=    -444.4784282       time=      15.57
 Minus side of path:                    1282 steps. Energy=    -445.2288580       time=      15.76

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.4784282 0.67959         -443.7988409  1.4300         -445.2288580   7.993   4.968  18.575  11.736
        Known (#6)                                              Known (#7)
 Unconnected minimum 6 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     967.86    
 decide> The unconnected minima in the chain and their distances are:
     2        7.85     6 
 

 tryconnect> 630-iteration DNEB run for minima 2_F and 6_S using 18 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      3.100679103    
 Double-ended search iterations= 630 RMS= 0.0286 Dev= 3.83% S= 10.35 time= 85.87
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):         28
 DNEB run yielded 1 true transition state(s) time=  28.11
 isnewts> transition state is the same as number        3 energy=     -442.1055986752
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=     1137.5    
 decide> The unconnected minima in the chain and their distances are:
     2        7.24     7 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 7_S using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      2.429463211    
 Double-ended search iterations= 805 RMS= 0.0562 Dev= 4.54% S= 12.73 time= 141.77
 Following    1 images are candidates for TS:   11  
 Converged to TS (number of iterations):         26
 DNEB run yielded 1 true transition state(s) time=  27.31
 isnewts> transition state is the same as number        3 energy=     -442.1055986752
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      1 missing connections, weight=     1451.8    
 decide> The unconnected minima in the chain and their distances are:
     2        7.85     6 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 6_S using 23 images  (DNEB attempt #3)  ...
 lbfgs> Final DNEB force constant      4.810170981    
 Double-ended search iterations= 805 RMS= 0.0747 Dev= 3.47% S= 10.24 time= 139.75
 Following    1 images are candidates for TS:   15  
 Converged to TS (number of iterations):         46
 DNEB run yielded 1 true transition state(s) time=  34.61
 isnewts> transition state is the same as number        3 energy=     -442.1055986752
 tryconnect> Will not repeat search for TS      1 same as TS      3
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 10 >>>>>>>>>>>>>>>>>>>>> 7 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=     1778.1    
 decide> The unconnected minima in the chain and their distances are:
     2        9.62     4 
 

 tryconnect> 770-iteration DNEB run for minima 2_F and 4_S using 22 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      6.768393620    
 Double-ended search iterations= 770 RMS= 0.0790 Dev= 3.32% S= 15.60 time= 127.54
 Following    2 images are candidates for TS:    6   18  
 Converged to TS (number of iterations):         39
 Converged to TS (number of iterations):         18
 DNEB run yielded 2 true transition state(s) time=  52.12
 isnewts> transition state is the same as number        3 energy=     -442.1055986752
 tryconnect> Will not repeat search for TS      1 same as TS      3
 isnewts> transition state is the same as number        5 energy=     -440.4795664169
 tryconnect> Try the path again for ts      2 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:                    1289 steps. Energy=    -445.2288580       time=      13.30
 Minus side of path:                    1316 steps. Energy=    -442.6434194       time=      13.88

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -445.2288580  4.7493         -440.4795664  2.1639         -442.6434194   8.399   7.209  19.582  11.133
        Known (#7)                                              Known (#4)
 Alternative path found between members of the S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 11 >>>>>>>>>>>>>>>>>>>>> 7 minima and 7 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      6 steps with      1 missing connections, weight=     1964.9    
 decide> The unconnected minima in the chain and their distances are:
     2       12.53     5 
 

 tryconnect> 105-iteration DNEB run for minima 2_F and 5_S using 3 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      3.589423646    
 Double-ended search iterations= 105 RMS= 0.0316 Dev= 0.03% S= 12.57 time= 2.60
 Following    1 images are candidates for TS:    3  
 Converged to TS (number of iterations):         33
 DNEB run yielded 1 true transition state(s) time=  26.82

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1295 steps. Energy=    -444.8146936       time=      13.32
 Minus side of path:                    1270 steps. Energy=    -444.5416270       time=      12.99

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.8146936 0.28865         -444.5260417 0.15585E-01     -444.5416270  12.646  12.527   4.867  44.795
        Known (#2)                                              Known (#5)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -446.4477589  5.2767        -441.1710404  3.6814        -444.8524861  15.750  12.927   8.498  25.652
   2     -444.8524861  3.7009        -441.1515646  1.4919        -442.6434194  10.525   9.091   9.836  22.163
   5     -442.6434194  2.1639        -440.4795664  4.7493        -445.2288580   8.399   7.208  19.652  11.093
   6     -445.2288580  1.4300        -443.7988409 0.67959        -444.4784282   7.993   4.968  18.575  11.736
   3     -444.4784282  2.3728        -442.1055987  2.4360        -444.5416270  14.840  10.749   8.242  26.450
   8     -444.5416270 0.15585E-01    -444.5260417 0.28865        -444.8146936  12.646  12.527   4.867  44.795

 Number of TS in the path       =      6
 Number of cycles               =     11

 Elapsed time=                              1245.87
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            115332 time=         859.83 %= 69.0
 OPTIM> # of energy+gradient+Hessian calls=       518 time=         150.38 %= 12.1
