
 OPTIM version 4.0, Copyright (C) 1999-2006 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 08/04/2009 at 01:07:08
  [-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> 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= 400, maximum tangent space steps=   5 or  100 at convergence
 fetchz> Uphill mode is    0 for initial step and    0 after that
 fetchz> Allowed steps for largest Hessian eigenvector= 100, smallest eigenvector=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> Convergence criterion for LBFGS optimization: RMS force< 0.10000000E-05 maximum steps= 10000
 fetchz> Maximum energy rise in LBFGS minimization=    0.1000000000E-03
 fetchz> Number of updates before reset in LBFGS= ****
 fetchz> Number of updates before reset in XLBFGS=   4
 fetchz> Number of updates before reset in mind=   5
 fetchz> Number of updates before reset in neb=   4
 fetchz> Initial guess for diagonal elements in LBFGS=     0.1000
 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=    -450.6226290     RMS force=    0.9630937901E-06
 OPTIM> Final energy  =    -450.9286588     RMS force=    0.9656185508E-06
 keep permutation
            4            3            2    22.29171805608949     
           45           47           46    21.05057579012269     
           47           46           45    21.03200190200479     
           47           45           46    20.41081785354356     
          165          167          166    13.83359584461751     
          213          215          214    12.22652272953851     
 KeyConnect> Maximum cycles = 50, maximum images = 61
 KeyConnect> Maximum attempts per pair of minima = 3, with increment image density of 3.00
 KeyConnect> Image density = 1.00, iteration density = 40.00
 KeyNEB> Initial and final NEB force constants      5.000000000         5.000000000     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 states candidates will be optimized
 KeyOutput> Concise printing during transition states optimization
 KeyOutput> Transition states candidates are maxima along NEB
 KeyMin> Maximal number of iterations will vary from call to call, 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
 KeyConnect> Using 30 images and 400 iterations in the first NEB run
 KeyDecide> Cost function in Dijkstra algorithm is Exp[D]

 >>>>>>>>>>>>>>>>>>>>> CONNECT CYCLE 1 >>>>>>>>>>>>>>>>>>>>> 2 minima and 0 ts are known >>>>>>>>>>>>>>>>>>>>
 decide> Shortest path in Dijkstra has      1 steps with      1 missing connections, length=     13.524    
 decide> The unconnected minima in the chain and their distances are:
     2       13.52     1 
 
 tryconnect> First DNEB calculation will use parameters from the NEWNEB line in odata

 >>>>>  400-iteration DNEB run for minima 1_S and 2_F using 30 images  ...
 intinterp> deall
 Double-ended search iterations= 400 RMS= 0.0794 Dev= 4.60% S= 17.78 time= 146.77
 Following    1 images are candidates for TS:   14  
 Converged to TS (number of iterations):         Total:   -446.083028718
    Total:   -446.041728660
    Total:   -446.024554274
    Total:   -446.025756576
    Total:   -446.081171997
    Total:   -446.083277356
    Total:   -446.144331620
    Total:   -446.145815941
    Total:   -446.199822768
    Total:   -446.205919767
    Total:   -446.301819242
    Total:   -446.305592951
    Total:   -446.349832624
    Total:   -446.351647589
    Total:   -446.388909742
    Total:   -446.389849723
    Total:   -446.408757520
    Total:   -446.409319176
    Total:   -446.421447942
    Total:   -446.422567392
    Total:   -446.440917171
    Total:   -446.442195973
    Total:   -446.463356768
    Total:   -446.463697445
    Total:   -446.467450413
    Total:   -446.467549044
   26.
 DNEB run yielded 1 true transition state(s) time=  55.47
  tryconnect> TS appears to be new

 >>>>>  Path run for ts 1 ...
 Plus  side of path:                    1330 steps. Energy=    -450.6226290                                time=      25.97
 Minus side of path:                    1318 steps. Energy=    -450.6177313                                time=      25.81

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.6226290  4.1551         -446.4675580  4.1502         -450.6177313  24.704   8.316  11.072  19.689
        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, length=     7.0648    
 decide> The unconnected minima in the chain and their distances are:
     2        7.06     3 
 

 >>>>>  280-iteration DNEB run for minima 2_F and 3_S using 7 images  ...
 intinterp> deall
 Double-ended search iterations= 280 RMS= 0.0084 Dev= 0.05% S= 7.08 time= 24.39
 Following    1 images are candidates for TS:    6  
 Converged to TS (number of iterations):         Total:   -450.613438641
    Total:   -450.613327126
    Total:   -450.613356674
    Total:   -450.613384180
    Total:   -450.613683489
    Total:   -450.613687698
    Total:   -450.613767105
    Total:   -450.613799041
    Total:   -450.613829078
    Total:   -450.613848463
    Total:   -450.613856219
    Total:   -450.613866961
    Total:   -450.613885544
    Total:   -450.613898997
    Total:   -450.613901567
    Total:   -450.613902211
    Total:   -450.613902785
   17.
 DNEB run yielded 1 true transition state(s) time=  47.28
  tryconnect> TS appears to be new

 >>>>>  Path run for ts 2 ...
 Plus  side of path:                    1262 steps. Energy=    -450.6177313                                time=      25.01
 Minus side of path:                    1312 steps. Energy=    -450.9286588                                time=      26.62

         E+        Ets - E+           Ets       Ets - E-           E-          S       D      gamma   ~N
     -450.6177313 0.38285E-02     -450.6139028 0.31476         -450.9286588   7.099   7.065   2.659  81.973
        Known (#3)                                              Known (#2)
 Connected path found
  ts        E+         Ets - E+          Ets       Ets - E-          E-          S       D      gamma   ~N
   1     -450.6226290  4.1551        -446.4675580  4.1502        -450.6177313  24.704   8.316  11.072  19.689
   2     -450.6177313 0.38285E-02    -450.6139028 0.31476        -450.9286588   7.099   7.065   2.659  81.973

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

 Elapsed time=                               377.46
 OPTIM> # of energy calls=                          0 time=           0.00 %=  0.0
 OPTIM> # of energy+gradient calls=             21814 time=         254.42 %= 67.4
 OPTIM> # of energy+gradient+Hessian calls=        43 time=          38.92 %= 10.3
FORTRAN STOP
