
 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 21:54:29
  [-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=    -444.6492050     RMS force=    0.9785130572E-06
 OPTIM> Final energy  =    -447.6246567     RMS force=    0.9238831814E-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=    0.28375E+06
 decide> The unconnected minima in the chain and their distances are:
     2       65.71     1 
 

 tryconnect> 665-iteration DNEB run for minima 1_S and 2_F using 19 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      14.07100423    
 Double-ended search iterations= 665 RMS= 1.9265 Dev= 2.19% S= 81.56 time= 96.73
 Following    1 images are candidates for TS:    9  
 Failed to converge to TS (number of iterations):        251
 DNEB run yielded 0 true transition state(s) time= 147.09
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 2 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, weight=    0.56750E+06
 decide> The unconnected minima in the chain and their distances are:
     2       65.71     1 
 

 tryconnect> 805-iteration DNEB run for minima 1_S and 2_F using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      9.523809524    
 Double-ended search iterations= 805 RMS= 0.5395 Dev= 2.06% S= 82.71 time= 139.04
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         67
 DNEB run yielded 1 true transition state(s) time=  65.80

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1297 steps. Energy=    -447.4459602       time=      13.71
 Minus side of path:                    1305 steps. Energy=    -448.3178221       time=      13.84

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.4459602 0.72245         -446.7235118  1.5943         -448.3178221   1.834   1.582 148.376   1.469
        *NEW* (Placed in 3)                                     *NEW* (Placed in 4)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 3 >>>>>>>>>>>>>>>>>>>>> 4 minima and 1 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      2 missing connections, weight=    0.18873E+06
 decide> The unconnected minima in the chain and their distances are:
     2       47.69     3     3       43.13     1 
 

 tryconnect> 490-iteration DNEB run for minima 2_F and 3_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      70.39988712    
 Double-ended search iterations= 734 RMS= 1.5160 Dev= 1.89% S= 85.07 time= 75.93
 Following    1 images are candidates for TS:    8  
 Converged to TS (number of iterations):         95
 DNEB run yielded 1 true transition state(s) time=  69.75
 tryconnect> Transition state with energy     -376.3952882     ignored

 tryconnect> 420-iteration DNEB run for minima 1_S and 3_U using 12 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant     0.1659964797    
 Double-ended search iterations= 420 RMS= 0.0948 Dev= 0.75% S= 45.89 time= 38.56
 Following    2 images are candidates for TS:    1    8  
 Converged to TS (number of iterations):         58
 bfgsts> WARNING *** initial eigenvalue is positive - increase NEBK?
 Converged to TS (number of iterations):        171
 DNEB run yielded 2 true transition state(s) time= 135.73

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1693 steps. Energy=    -448.3178221       time=      21.20
 Minus side of path:                    1280 steps. Energy=    -444.6492050       time=      13.85

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.3178221  3.7180         -444.5997857 0.49419E-01     -444.6492050  44.757  43.253   1.681 129.670
        Known (#4)                                              Known (#1)
 Unconnected minimum 4 found its way to S set.

 >>>>>  Path run for ts 3 ...
 Plus  side of path:                    1460 steps. Energy=    -450.6383416       time=      17.01
 Minus side of path:                    1316 steps. Energy=    -447.4459602       time=      14.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.6383416  3.4263         -447.2120589 0.23390         -447.4459602  40.901  38.822   3.591  60.709
        *NEW* (Placed in 5)                                     Known (#3)
 Unconnected minimum 5 found its way to S set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 4 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.10877E+06
 decide> The unconnected minima in the chain and their distances are:
     2       47.74     4 
 

 tryconnect> 490-iteration DNEB run for minima 2_F and 4_S using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      70.39988712    
 Double-ended search iterations= 544 RMS= 3.3635 Dev= 2.69% S= 79.44 time= 55.99
 Following    1 images are candidates for TS:    9  
 Converged to TS (number of iterations):         96
 DNEB run yielded 1 true transition state(s) time=  60.99
 tryconnect> Transition state with energy     -370.7587099     ignored
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 5 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.21696E+06
 decide> The unconnected minima in the chain and their distances are:
     2       47.69     3 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 3_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      25.26950195    
 Double-ended search iterations= 1599 RMS= 0.6266 Dev= 5.65% S= 105.08 time= 273.48
 Following    1 images are candidates for TS:   12  
 Converged to TS (number of iterations):        108
 DNEB run yielded 1 true transition state(s) time=  65.02
 tryconnect> Transition state with energy     -382.0536258     ignored
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 6 >>>>>>>>>>>>>>>>>>>>> 5 minima and 3 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      2 steps with      1 missing connections, weight=    0.21754E+06
 decide> The unconnected minima in the chain and their distances are:
     2       47.74     4 
 

 tryconnect> 805-iteration DNEB run for minima 2_F and 4_S using 23 images  (DNEB attempt #2)  ...
 lbfgs> Final DNEB force constant      319.4774681    
 Double-ended search iterations= 1263 RMS= 0.7727 Dev= 3.74% S= 104.67 time= 215.19
 Following    3 images are candidates for TS:    5   14   21  
 Converged to TS (number of iterations):         48
 Converged to TS (number of iterations):        175
 Converged to TS (number of iterations):        108
 DNEB run yielded 3 true transition state(s) time= 199.89

 >>>>>  Path run for ts 4 ...
 Plus  side of path:                    1333 steps. Energy=    -447.5485391       time=      14.38
 Minus side of path:                    1314 steps. Energy=    -448.2493470       time=      14.09

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -447.5485391 0.86201         -446.6865328  1.5628         -448.2493470   3.442   3.205  26.783   8.139
        *NEW* (Placed in 6)                                     *NEW* (Placed in 7)
 Connection established between members of the U set.

 >>>>>  Path run for ts 5 ...
 Plus  side of path:                    1425 steps. Energy=    -444.6484274       time=      15.66
 Minus side of path:                    1477 steps. Energy=    -433.9708650       time=      16.46

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -444.6484274  23.886         -420.7622827  13.209         -433.9708650  37.452  26.235   5.506  39.596
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues     10    11
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues     11    12
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom    173
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom    197
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues     11    12
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom    197
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -420.7622827     ignored, cis-trans isomerisation detected in one or more peptide bonds.

 >>>>>  Path run for ts 6 ...
 Plus  side of path:                    1312 steps. Energy=    -450.6468359       time=      13.95
 Minus side of path:                    1324 steps. Energy=    -447.6989509       time=      14.05

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.6468359  5.5225         -445.1243081  2.5746         -447.6989509  24.634  22.191   5.507  39.587
        *NEW* (Placed in 8)                                     *NEW* (Placed in 9)
 Connection established between members of the U set.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 7 >>>>>>>>>>>>>>>>>>>>> 9 minima and 6 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      5 steps with      2 missing connections, weight=    0.11487E+06
 decide> The unconnected minima in the chain and their distances are:
     2        7.94     7     6       48.54     3 
 

 tryconnect> 70-iteration DNEB run for minima 2_F and 7_U using 2 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      5.050679530    
 Double-ended search iterations= 70 RMS= 0.1973 Dev= 0.30% S= 8.65 time= 1.07
 Following    1 images are candidates for TS:    1  
 Converged to TS (number of iterations):         30
 DNEB run yielded 1 true transition state(s) time=  26.02

 >>>>>  Path run for ts 7 ...
 Plus  side of path:                    1298 steps. Energy=    -448.3339633       time=      13.81
 Minus side of path:                    1292 steps. Energy=    -447.6246567       time=      13.72

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -448.3339633  1.5673         -446.7667129 0.85794         -447.6246567   3.314   3.082  32.810   6.644
        *NEW* (Placed in 10)                                    Known (#2)
 Unconnected minimum 10 found its way to F set.

 tryconnect> 490-iteration DNEB run for minima 3_S and 6_U using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      139.3869611    
 Double-ended search iterations= 490 RMS= 5.6124 Dev= 1.99% S= 83.52 time= 50.65
 Following    1 images are candidates for TS:    7  
 Converged to TS (number of iterations):         74
 DNEB run yielded 1 true transition state(s) time=  45.25

 >>>>>  Path run for ts 8 ...
 Plus  side of path:                    1356 steps. Energy=    -442.6789433       time=      14.79
 Minus side of path:                    1331 steps. Energy=    -442.6789433       time=      14.30

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -442.6789433  3.8243         -438.8545942  3.8243         -442.6789433  32.284   3.071  72.639   3.001
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues     11    12
 tryconnect> MINUS minimum: cis-trans isomerisation of a peptide bond detected involving atom    197
check_cistrans_protein>  WARNING -- cis (or deformed) peptide bond detected between residues     11    12
 tryconnect> PLUS minimum: cis-trans isomerisation of a peptide bond detected involving atom    197
 tryconnect> Cis-trans isomerisation of a peptide bond detected (wrt. the original structure), rejecting
 tryconnect> Transition state with energy     -438.8545942     ignored, cis-trans isomerisation detected in one or more peptide bonds.
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 8 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      4 steps with      1 missing connections, weight=    0.10756E+06
 decide> The unconnected minima in the chain and their distances are:
    10       47.56     3 
 

 tryconnect> 490-iteration DNEB run for minima 3_S and 10_F using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      449.5368804    
 Double-ended search iterations= 847 RMS= 2.5168 Dev= 3.03% S= 80.81 time= 87.76
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):        117
 DNEB run yielded 1 true transition state(s) time=  77.28
 tryconnect> Transition state with energy     -378.0297409     ignored
 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 9 >>>>>>>>>>>>>>>>>>>>> 10 minima and 8 ts are known >>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      3 steps with      1 missing connections, weight=    0.10764E+06
 decide> The unconnected minima in the chain and their distances are:
    10       47.57     4 
 

 tryconnect> 490-iteration DNEB run for minima 4_S and 10_F using 14 images  (DNEB attempt #1)  ...
 lbfgs> Final DNEB force constant      169.4257224    
 Double-ended search iterations= 735 RMS= 1.7842 Dev= 2.16% S= 84.54 time= 75.86
 Following    1 images are candidates for TS:    7  
