    
  __________DelPhi V. 4 Release 1.0_______________  
 |                                                | 
 | A program to solve the PB equation             | 
 | in 3D, using non-linear form, incorporating    | 
 | many dielectric regions, multisalt ionic       | 
 | strength, different probe radii, periodic      | 
 | and focussing boundary conditions, utilizing   | 
 | stripped optimum successive over-relaxation    | 
 | and an improved algorithm for mapping the      | 
 | Mol. Surface to the finite-Difference grid     | 
 | Recompiled on Linux and PC                     | 
 |    January 2002 --------  Walter Rocchia       | 
 |__________________           ___________________| 
                    DelPhi V. 4                     
   
  program started on Wed Sep 29 2004
              at 18:02:45
 opening parameter file fort.10
 atom radii read from file
 gln.siz
  
 !this is amber 94 parameters defined by amber               
 !you can find charge in /usr/local/amber7/dat/leap/lib/ all_
 !you can find radii in /usr/local/amber7/dat/leap/parm parm9
 !THIS FILE ONLY INCLUDES THE AMINO ACID WHICH ARE INCLUDED I
 !NOT THE TOTAL 25 AMINO ACID                                
 # of radius parameter records:          17
  
 atomic charges read from file
 gln.crg
  
 !this is amber 94 parameters defined by amber               
 !you can find charge in /usr/local/amber7/dat/leap/lib/ all_
 !you can find radii in /usr/local/amber7/dat/leap/parm parm9
 !THIS FILE ONLY INCLUDES THE AMINO ACID WHICH ARE INCLUDED I
 !NOT THE TOTAL 25 AMINO ACID                                
 # of charge parameter records:          17
 assigning charges and radii...
  
 opening formatted file:gln.pdb
 You are not reading from an objectfile! assuming     having only molecules, and one dielectric medium
 number of atoms read in =           17
  
  
 Direct mapping of epsilon: (0/1)(n/y)           1
 time to read in and/or assign rad/chrg=  0.0000000E+00
 object number :              1,  is a molecule
 modifying midpoints using frc input file
   
 grid size                  :          81
 percent of box to be filled:   12.50709    
 scale,in grids/A :   1.000000    
 xmin,xmax     (A):   43.67200       50.62000    
 ymin,ymax     (A):   46.30100       52.49300    
 zmin,zmax     (A):   31.33900       41.13200    
 x,y,z range   (A):    6.948002       6.192001       9.793001    
 system geometric center in (A):   47.14600       49.39700       36.23550    
  grid  box is centered in (A) :   46.98117       49.33470       36.19170    
 object centred at (gu)     :   999.0000      0.0000000E+00  0.0000000E+00
 outer dielectric           :   80.00000    
 dielectric in medium number           1 :   1.000000    
 first kind salt concentration (M)   :  0.0000000E+00
 valences salt 1 are                   1 and           1
 second kind salt concentration (M)  :  0.0000000E+00
 valences salt 2 are                   0 and           0
 ionic strength (M)         :  0.0000000E+00
 debye length (A)           :   1000000.    
 ion exclusion radius (A)   :   1.824000    
 probe radius facing water(A:   1.400000    
 probe radius, internal (A) :   1.400000    
 boundary conditions        : dipolar  
 x,y,z periodic bc. flags   : F F F
 # of linear iterations     :        1200
 convergence by rms change :  1.0000000E-06 kt
 convergence by max change :  0.0000000E+00 kt
 # of non-linear iterations :           0
 non-linear energy calculat.: F
 manual relaxation parameter : F
 ionic direct energy contribution: F
 concentration map output   : F
 spherical charge distbn.   : F
 INSIGHT format output      : F
 site potential output      : F
 modified atom file output  : F
 map file label             :
qdiffxas: qdiffxs4 with an improved surfacing routine       
  convergence graph turned off
  potential listings turned off
  
 start vw surface at   0.0000000E+00
 Starting creating Vand der Waals  Epsilon Map 
 Ending creating Vand der Waals  Epsilon Map 
 fill in re-entrant regions at   0.0000000E+00
 boundary points facing continuum solvent=          137
 total number of boundary points before elab.=          137
 reading accessible surface arcs data from file       ARCDAT
 no. of arc points read =         1160
 grid for indexing accessible points =    1.400000    
 bgp added m=           6 bgp removed  mr =           9
 bgp added m=           0 bgp removed  mr =           0
 time to grow re-entrant surface =   0.0000000E+00
 no. cavity mid-points inaccessible to solvent =            0
 after surface elaboration ibnum=          134
     and               ibnumsurf=          134
 scaling boundary grid points
 % of boundary points contacting solvent =    60.44776    
 time taken =   0.0000000E+00
            0 points had to be assigned by global comparison
 time to turn everything in is  0.0000000E+00
 number of charges coming from molecules           17
 number of charge distrib. present            0
   
 number of atom coordinates read  :           17
 total number of assigned charges    :           17
 net assigned charge              :   0.0000000E+00
 assigned positive charge         :    2.604100    
 centred at (gu) :   41.04630       40.95641       40.27691    
 assigned negative charge         :   -2.604100    
 centred at (gu) :   41.43821       40.82837       40.51801    
    
 number of dielectric boundary points         134
 no. dielectric boundary points in salt =            0
 no. grid points charged and not internal=          21
 ## out of them,           2 charged points    are in solution ##
 iepsmp to db, and charging done at  9.9999998E-03
 number of grid points assigned charge          94
  
   setting boundary conditions
  
  some initial phi values: 
  midg,midg,1; midg,midg,igrid 
   2.8687366E-03 -2.6407752E-03
  midg,1,midg; midg,igrid,midg 
  -1.4830766E-03  1.4386462E-03
  1,midg,midg; igrid,midg,midg 
   4.3810015E-03 -4.5643286E-03
  
gauss-seidel spectral radius is        0.9984518290
  
 estimated iterations to convergence         202
   
 setup time was (sec)   2.9999999E-02
   
 now iterating at: 18:02:45
  
  
   rms-change     max change       #iterations
    552939.8       233.2755     at          10 iterations
    103850.3       105.8212     at          20 iterations
    17036.59       49.19054     at          30 iterations
    3875.195       23.01592     at          40 iterations
    498.4704       7.067528     at          50 iterations
    116.7615       4.118553     at          60 iterations
    21.72808       1.740335     at          70 iterations
    4.872394      0.8811264     at          80 iterations
   0.8931702      0.2975388     at          90 iterations
   0.1443471      0.1240292     at         100 iterations
   2.5604703E-02  5.5797577E-02 at         110 iterations
   3.6827947E-03  1.8668175E-02 at         120 iterations
   6.9815479E-04  8.4934235E-03 at         130 iterations
   1.4399042E-04  4.2114258E-03 at         140 iterations
   2.9033956E-05  2.1362305E-03 at         150 iterations
   5.8221590E-06  9.4604492E-04 at         160 iterations
   1.1765728E-06  4.5776367E-04 at         170 iterations
   1.9340712E-07  1.6403198E-04 at         180 iterations
 finished qdiffx linear iterations
 at                       : 18:02:46
 total time elapsed so far:    1.010000    
 # loops                  :          180
 mean,max change (kT/e)   :   1.9340712E-07  1.6403198E-04
  
 total grid energy          :        588.0082     kt
 self-reaction field energy :      1.4612769E-05 kt
 total s.charge,no epsin carrying :    0.0023
 corrected reaction field energy:   -39.05563     kt
 total reaction field energy :     -39.05561     kt
  
 coulombic energy :                -880.8419     kt
 All energy terms but grid and self_react.:  -919.8975    kt
 energy calculations done at   1.010000    
   
 writing potential map in DELPHI format
   
 potential map written to file
 fort.14                                                                         
   
   
 total cpu time was (sec)    1.010000    
   
 DelPhi exited at 18:02:46
