
 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 18:21:49
  [-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


 OPTIM> Using translational/rotational ev shift=     1000000.000    
 OPTIM> Initial energy=    -451.4537995     RMS force=    0.9183379396E-06
 OPTIM> Final energy  =    -450.4708986     RMS force=    0.9670578179E-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=    0.44992E+06
 decide> The unconnected minima in the chain and their distances are:
     2       76.63     1 
 

 tryconnect> 770-iteration DNEB run for minima 1_S and 2_F using 22 images  (DNEB attempt #1)  ...
 lbfgs> Cold fusion diagnosed - step discarded, energy, limit=    -1003249.342        -1000000.000    
 lbfgs> Final DNEB force constant      73.91988148    
 Double-ended search iterations= 258 RMS= 289897258680.3250 Dev= 52.08% S= 136.63 time= 30.49
 Following    2 images are candidates for TS:   10   12  
 mylbfgs> Too many failures - give up
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 Failed to converge to TS (number of iterations):        251
 Converged to TS (number of iterations):         76
 DNEB run yielded 1 true transition state(s) time= 544.87
 tryconnect> Transition state with energy     -382.9484336     ignored
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.89983E+06
 decide> The unconnected minima in the chain and their distances are:
     2       76.63     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      73.91988148    
 Double-ended search iterations= 805 RMS= 2.5989 Dev= 1.90% S= 115.72 time= 134.37
 Following    6 images are candidates for TS:    5    7    9   13   16   19  
 Converged to TS (number of iterations):        172
 Converged to TS (number of iterations):         55
 Converged to TS (number of iterations):        123
 Converged to TS (number of iterations):         75
 Converged to TS (number of iterations):         98
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 5 true transition state(s) time= 492.37

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1365 steps. Energy=    -443.6390333       time=      14.54
 Minus side of path:                    1422 steps. Energy=    -450.4403261       time=      15.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -443.6390333  1.2579         -442.3810907  8.0592         -450.4403261  40.845  36.940   6.246  34.902
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1258 steps. Energy=    -441.2532440       time=      12.95
 Minus side of path:                    1265 steps. Energy=    -441.5991391       time=      13.08

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -441.2532440 0.39653         -440.8567136 0.74243         -441.5991391   2.005   1.791  82.442   2.644
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      2     3
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     39
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      2     3
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     39
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -440.8567136     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1801 steps. Energy=    -438.3651281       time=      22.60
 Minus side of path:                    1339 steps. Energy=    -433.3915731       time=      14.52

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -438.3651281  23.469         -414.8965647  18.495         -433.3915731  48.064  24.333   9.615  22.672
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      2     3
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     39
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      2     3
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     39
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -414.8965647     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1259 steps. Energy=    -444.1756019       time=      13.27
 Minus side of path:                    1259 steps. Energy=    -444.1756019       time=      13.21

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.1756019  3.4776         -440.6979773  3.4776         -444.1756019   4.037   3.071  72.524   3.006
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      2     3
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     39
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      2     3
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     39
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -440.6979773     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1269 steps. Energy=    -439.1545579       time=      13.35
 Minus side of path:                    1125 steps. Energy=    -437.8032991       time=      12.31

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -439.1545579  1.4195         -437.7350202 0.68279E-01     -437.8032991   1.379   1.305 207.119   1.053
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      2     3
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     39
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues      2     3
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom     39
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -437.7350202     ignored, cis-trans isomerisation detected in one or more peptide bonds.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 5 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=    0.31934E+06
 decide> The unconnected minima in the chain and their distances are:
     2       50.46     4     4       57.57     1 
 

 tryconnect> 525-iteration DNEB run for minima 2_F and 4_U using 15 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.5958316896E-01
 Double-ended search iterations= 525 RMS= 0.0145 Dev= 3.02% S= 55.49 time= 59.14
 Following    2 images are candidates for TS:    6   11  
 Converged to TS (number of iterations):         30
 Converged to TS (number of iterations):        170
 DNEB run yielded 2 true transition state(s) time= 121.95

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1452 steps. Energy=    -450.4708986       time=      19.35
 Minus side of path:                    1519 steps. Energy=    -450.9727420       time=      20.96

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.4708986 0.93133         -449.5395712  1.4332         -450.9727420  55.969  51.440   2.037 107.004
        Known (#2)                                              *NEW* (Placed in 5)
 Unconnected minimum 5 found its way to F set.

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1447 steps. Energy=    -449.9360237       time=      16.71
 Minus side of path:                    1511 steps. Energy=    -450.4403261       time=      16.98

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -449.9360237 0.92460         -449.0114266  1.4289         -450.4403261  55.630  51.271   2.094 104.102
        *NEW* (Placed in 6)                                     Known (#4)
 Connection established between members of the U set.

 tryconnect> 595-iteration DNEB run for minima 1_S and 4_U using 17 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.3009354918E-01
 Double-ended search iterations= 595 RMS= 0.0461 Dev= 2.85% S= 67.54 time= 74.52
 Following    2 images are candidates for TS:    9   11  
 Converged to TS (number of iterations):         48
 Converged to TS (number of iterations):         80
 DNEB run yielded 2 true transition state(s) time=  83.81

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1521 steps. Energy=    -450.9727420       time=      17.46
 Minus side of path:                    1550 steps. Energy=    -451.4537995       time=      17.55

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.9727420  1.6264         -449.3463234  2.1075         -451.4537995  62.038  57.712   3.436  63.438
        Known (#5)                                              Known (#1)

 >>>>>  Path run for ts 9 ...
 Plus  side of path:                    1256 steps. Energy=    -450.4403261       time=      13.28
 Minus side of path:                    1286 steps. Energy=    -450.9727420       time=      13.24

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.4403261 0.40641         -450.0339174 0.93882         -450.9727420   8.378   8.005  19.127  11.397
        Known (#4)                                              Known (#5)
 Unconnected minimum 4 found its way to F set.
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   8     -451.4537995  2.1075        -449.3463234  1.6264        -450.9727420  62.038  57.712   3.436  63.438
   6     -450.9727420  1.4332        -449.5395712 0.93133        -450.4708986  55.969  51.440   2.037 107.004

 Number of TS in the path       =      2
 Number of cycles               =      3

 Elapsed time=                              1822.83
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=            135809 time=         999.46 %= 54.8
 OPTIM> # of energy+gradient+Hessian calls=      1427 time=         403.41 %= 22.1
