
 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 22:15:22
  [-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=    -450.4905590     RMS force=    0.9602289674E-06
 OPTIM> Final energy  =    -445.1484190     RMS force=    0.9430713196E-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     1    6 from     0.47102E-02 to     0.47931E-02 ref=     2.0984    
 checkperc> Increasing con cutoff atoms     1    7 from     0.80095E-02 to     0.81169E-02 ref=     2.4993    
 checkperc> Increasing con cutoff atoms     1    8 from     0.55836E-01 to     0.56138E-01 ref=     2.7298    
 checkperc> Increasing con cutoff atoms     1   12 from     0.72996E-02 to     0.77386E-02 ref=     2.4931    
 checkperc> Increasing con cutoff atoms     2    4 from     0.31571E-02 to     0.31611E-02 ref=     1.6370    
 checkperc> Increasing con cutoff atoms     2    5 from     0.48118E-02 to     0.49170E-02 ref=     2.0723    
 checkperc> Increasing con cutoff atoms     2   12 from     0.33735E-01 to     0.34529E-01 ref=     2.7114    
 checkperc> Increasing con cutoff atoms     3    7 from     0.72729E-02 to     0.74082E-02 ref=     3.3770    
 checkperc> Increasing con cutoff atoms     4    6 from     0.14867E-01 to     0.15077E-01 ref=     2.4010    
 checkperc> Increasing con cutoff atoms     4   12 from     0.76126E-02 to     0.79649E-02 ref=     3.3642    
 checkperc> Increasing con cutoff atoms     5    7 from     0.19374E-02 to     0.19762E-02 ref=     1.5360    
 checkperc> Increasing con cutoff atoms     5   12 from     0.22413E-02 to     0.23512E-02 ref=     1.5304    
 checkperc> Increasing con cutoff atoms     5   13 from     0.58711E-02 to     0.59082E-02 ref=     2.3997    
 checkperc> Increasing con cutoff atoms     5   14 from     0.16452E-01 to     0.17138E-01 ref=     2.4647    
 checkperc> Increasing con cutoff atoms     5   15 from     0.44900E-01 to     0.46732E-01 ref=     2.5806    
 checkperc> Increasing con cutoff atoms     6   12 from     0.94948E-02 to     0.96049E-02 ref=     2.1259    
 checkperc> Increasing con cutoff atoms     7    8 from     0.41463E-03 to     0.41749E-03 ref=     1.0919    
 checkperc> Increasing con cutoff atoms     7   11 from     0.39288E-02 to     0.39444E-02 ref=     1.9685    
 checkperc> Increasing con cutoff atoms     7   12 from     0.19193E-01 to     0.19569E-01 ref=     2.5255    
 checkperc> Increasing con cutoff atoms     9   11 from     0.61001E-01 to     0.61609E-01 ref=     2.2570    
 checkperc> Increasing con cutoff atoms    10   11 from     0.36808E-03 to     0.37165E-03 ref=    0.98136    
 checkperc> Increasing con cutoff atoms    12   15 from     0.12074E-01 to     0.12542E-01 ref=     2.0277    
 checkperc> Increasing con cutoff atoms    12   16 from     0.24344E-01 to     0.25362E-01 ref=     2.5098    
 checkperc> Increasing con cutoff atoms    13   14 from     0.10704E-01 to     0.11131E-01 ref=     2.2570    
 checkperc> Increasing con cutoff atoms    13   16 from     0.57295E-01 to     0.60711E-01 ref=     2.8688    
 checkperc> Increasing con cutoff atoms    16   18 from     0.42975E-02 to     0.50191E-02 ref=     1.5409    
 checkperc> Increasing con cutoff atoms    16   21 from     0.22654E-01 to     0.34924E-01 ref=     2.5800    
 checkperc> Increasing con cutoff atoms    18   21 from     0.14649E-02 to     0.20864E-02 ref=     1.4997    
 checkperc> Increasing con cutoff atoms    18   24 from     0.46529E-02 to     0.49875E-02 ref=     3.6846    
 checkperc> Increasing con cutoff atoms    18   25 from     0.82652E-02 to     0.11720E-01 ref=     4.5919    
 checkperc> Increasing con cutoff atoms    18   26 from     0.50240E-02 to     0.54163E-02 ref=     3.8121    
 checkperc> Increasing con cutoff atoms    18   27 from     0.69953E-02 to     0.74148E-02 ref=     5.0991    
 checkperc> Increasing con cutoff atoms    18   32 from     0.14109E-01 to     0.15275E-01 ref=     5.5209    
 checkperc> Increasing con cutoff atoms    19   20 from     0.54727E-02 to     0.94063E-02 ref=     1.7534    
 checkperc> Increasing con cutoff atoms    20   36 from     0.91757E-01 to     0.11843     ref=     2.7033    
 checkperc> Increasing con cutoff atoms    21   22 from     0.10682E-02 to     0.12577E-02 ref=     1.3517    
 checkperc> Increasing con cutoff atoms    21   24 from     0.26888E-02 to     0.27622E-02 ref=     2.2352    
 checkperc> Increasing con cutoff atoms    21   25 from     0.74080E-02 to     0.98124E-02 ref=     3.1995    
 checkperc> Increasing con cutoff atoms    21   32 from     0.43722E-02 to     0.47634E-02 ref=     4.7956    
 checkperc> Increasing con cutoff atoms    21   33 from     0.30076E-02 to     0.32987E-02 ref=     2.6548    
 checkperc> Increasing con cutoff atoms    21   34 from     0.44130E-02 to     0.49615E-02 ref=     2.9736    
 checkperc> Increasing con cutoff atoms    22   25 from     0.59001E-02 to     0.91901E-02 ref=     2.1146    
 checkperc> Increasing con cutoff atoms    22   33 from     0.14967E-02 to     0.23179E-02 ref=     3.6457    
 checkperc> Increasing con cutoff atoms    22   34 from     0.29040E-02 to     0.38171E-02 ref=     4.1911    
 checkperc> Increasing con cutoff atoms    23   25 from     0.68780E-02 to     0.12281E-01 ref=     2.5636    
 checkperc> Increasing con cutoff atoms    23   33 from     0.18876E-02 to     0.27838E-02 ref=     4.6796    
 checkperc> Increasing con cutoff atoms    23   34 from     0.36344E-02 to     0.53816E-02 ref=     5.1294    
 checkperc> Increasing con cutoff atoms    24   25 from     0.55957E-02 to     0.57126E-02 ref=     1.0185    
 checkperc> Increasing con cutoff atoms    24   33 from     0.16194E-02 to     0.18021E-02 ref=     3.5423    
 checkperc> Increasing con cutoff atoms    24   35 from     0.16543E-02 to     0.22737E-02 ref=     2.2183    
 checkperc> Increasing con cutoff atoms    25   28 from     0.12529E-01 to     0.16399E-01 ref=     2.8914    
 checkperc> Increasing con cutoff atoms    25   34 from     0.60206E-02 to     0.69105E-02 ref=     5.3614    
 checkperc> Increasing con cutoff atoms    25   35 from     0.60053E-02 to     0.65385E-02 ref=     3.2083    
 checkperc> Increasing con cutoff atoms    26   35 from     0.78530E-03 to     0.12014E-02 ref=     1.4283    
 checkperc> Increasing con cutoff atoms    27   28 from     0.12483E-02 to     0.22883E-02 ref=     1.0804    
 checkperc> Increasing con cutoff atoms    27   35 from     0.19455E-02 to     0.24662E-02 ref=     2.4820    
 checkperc> Increasing con cutoff atoms    28   29 from     0.27516E-02 to     0.41554E-02 ref=     2.1631    
 checkperc> Increasing con cutoff atoms    28   30 from     0.38496E-02 to     0.45492E-02 ref=     2.4960    
 checkperc> Increasing con cutoff atoms    28   31 from     0.25380E-02 to     0.42185E-02 ref=     3.4147    
 checkperc> Increasing con cutoff atoms    28   32 from     0.33087E-02 to     0.36463E-02 ref=     4.3086    
 checkperc> Increasing con cutoff atoms    28   33 from     0.29113E-02 to     0.36276E-02 ref=     3.9012    
 checkperc> Increasing con cutoff atoms    28   34 from     0.28671E-02 to     0.33627E-02 ref=     4.9817    
 checkperc> Increasing con cutoff atoms    29   32 from     0.29791E-02 to     0.29914E-02 ref=     2.1566    
 checkperc> Increasing con cutoff atoms    29   33 from     0.99951E-03 to     0.10561E-02 ref=     2.4452    
 checkperc> Increasing con cutoff atoms    32   33 from     0.21779E-02 to     0.23421E-02 ref=     2.1594    
 checkperc> Increasing con cutoff atoms    32   34 from     0.30298E-02 to     0.37470E-02 ref=     2.4783    
 checkperc> Increasing con cutoff atoms    33   35 from     0.59619E-03 to     0.62631E-03 ref=     1.4130    
 checkperc> Increasing con cutoff atoms    36   38 from     0.23735E-02 to     0.37594E-02 ref=     1.3421    
 checkperc> Increasing con cutoff atoms    37   38 from     0.76784E-02 to     0.98129E-02 ref=     2.2620    
 checkperc> Increasing con cutoff atoms    40   42 from     0.40228E-02 to     0.45093E-02 ref=     1.5380    
 checkperc> Increasing con cutoff atoms    40   48 from     0.26768E-01 to     0.28113E-01 ref=     2.4207    
 checkperc> Increasing con cutoff atoms    40   52 from     0.19969E-01 to     0.20152E-01 ref=     2.4482    
 checkperc> Increasing con cutoff atoms    40   53 from     0.34446E-01 to     0.41455E-01 ref=     2.5464    
 checkperc> Increasing con cutoff atoms    44   45 from     0.95035E-03 to     0.10645E-02 ref=     1.0894    
 checkperc> Increasing con cutoff atoms    44   46 from     0.19209E-03 to     0.22418E-03 ref=     1.0904    
 checkperc> Increasing con cutoff atoms    44   48 from     0.16213E-01 to     0.20771E-01 ref=     2.3802    
 checkperc> Increasing con cutoff atoms    45   48 from     0.10581E-01 to     0.13967E-01 ref=     3.3269    
 checkperc> Increasing con cutoff atoms    48   49 from     0.65158E-03 to     0.83437E-03 ref=    0.97632    
 checkperc> Increasing con cutoff atoms    50   52 from     0.29445E-02 to     0.40197E-02 ref=     1.3367    
 checkperc> Increasing con cutoff atoms    50   53 from     0.11038E-01 to     0.13804E-01 ref=     2.0107    
 checkperc> Increasing con cutoff atoms    52   54 from     0.33738E-02 to     0.44532E-02 ref=     1.4684    
 checkperc> Increasing con cutoff atoms    74   79 from     0.74379E-01 to     0.85499E-01 ref=     2.6879    
 checkperc> Increasing con cutoff atoms    78   80 from     0.55074E-02 to     0.81280E-02 ref=     1.5425    
 checkperc> Increasing con cutoff atoms    78   81 from     0.10242E-01 to     0.13392E-01 ref=     2.1605    
 checkperc> Increasing con cutoff atoms    78   82 from     0.15545E-01 to     0.29958E-01 ref=     2.1552    
 checkperc> Increasing con cutoff atoms    79   80 from     0.18073E-01 to     0.18525E-01 ref=     2.1490    
 checkperc> Increasing con cutoff atoms    81   82 from     0.11286E-01 to     0.19486E-01 ref=     1.7604    
 checkperc> Increasing con cutoff atoms    82   89 from     0.12266     to     0.13002     ref=     2.6624    
 checkperc> Increasing con cutoff atoms    89   90 from     0.39812E-02 to     0.41221E-02 ref=     1.2314    
 checkperc> Increasing con cutoff atoms    91   92 from     0.34471E-02 to     0.67961E-02 ref=     1.0123    
 checkperc> Increasing con cutoff atoms    91   93 from     0.42498E-02 to     0.53374E-02 ref=     1.4706    
 checkperc> Increasing con cutoff atoms   106  107 from     0.10944E-01 to     0.11834E-01 ref=     2.1418    
 checkperc> Increasing con cutoff atoms   116  117 from     0.10843E-02 to     0.14438E-02 ref=     1.0916    
 checkperc> Increasing con cutoff atoms   147  148 from     0.21006E-02 to     0.21375E-02 ref=     1.0794    
 checkperc> Increasing con cutoff atoms   148  153 from     0.52109E-02 to     0.52596E-02 ref=     3.8978    
 checkperc> Increasing con cutoff atoms   148  154 from     0.91525E-02 to     0.93283E-02 ref=     4.9748    
 checkperc> Increasing con cutoff atoms   162  163 from     0.82638E-03 to     0.13962E-02 ref=     1.0926    
 initialise> Interpolation metric value for minima 1 and 2 is      40.36542965    
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=     63596.    
 decide> The unconnected minima in the chain and their distances are:
     2       39.88     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=    17
 intlbfgs> constrained potential finished, time=       0.0
 intlbfgs> switch on true potential at step    335 fraction=    0.990000 images=     4 time=       0.9
 intlbfgs> Allowing     25 further optimization steps
 intlbfgs> After    360 steps, energy/image=    -433.4183093     RMS=.8940333589     images=   5
 intlbfgs> First  minimum number      1
 intlbfgs> Second minimum number      2
 intlbfgs> DNEB for minima      1     2 dist=   40.84     Attempts, images and iterations=     0    12   420
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.1065 Dev= 1.92% S= 42.24 time= 37.54
 Following    1 images are candidates for TS:   10  
 Converged to TS (number of iterations):         47
 DNEB run yielded 1 true transition state(s) time=  34.46

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1762 steps. Energy=    -450.4905590       time=      22.94
 Minus side of path:                    1276 steps. Energy=    -445.1484190       time=      14.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.4905590  5.6478         -444.8427352 0.30568         -445.1484190  44.797  39.928   2.594  84.049
        Known (#1)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -450.4905590  5.6478        -444.8427352 0.30568        -445.1484190  44.797  39.928   2.594  84.049

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

 Elapsed time=                               111.02
 OPTIM> # of energy calls=                          2 time=           0.01 %=  0.0
 OPTIM> # of energy+gradient calls=              9471 time=          69.83 %= 62.9
 OPTIM> # of energy+gradient+Hessian calls=        47 time=          13.87 %= 12.5
