    
  __________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 18:02:46
 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:   50.02835    
 scale,in grids/A :   4.000000    
 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   9.9999998E-03
 boundary points facing continuum solvent=         2299
 total number of boundary points before elab.=         2299
 reading accessible surface arcs data from file       ARCDAT
 no. of arc points read =         1160
 grid for indexing accessible points =    1.400000    
 bgp added m=         345 bgp removed  mr =         444
 bgp added m=          29 bgp removed  mr =          58
 bgp added m=           0 bgp removed  mr =           0
 time to grow re-entrant surface =   9.9999998E-03
 no. cavity mid-points inaccessible to solvent =            0
 after surface elaboration ibnum=         2171
     and               ibnumsurf=         2171
 scaling boundary grid points
 % of boundary points contacting solvent =    60.43298    
 time taken =   9.9999998E-03
            0 points had to be assigned by global comparison
 time to turn everything in is  4.9999997E-02
 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) :   41.18520       40.82565       38.10762    
 assigned negative charge         :   -2.604100    
 centred at (gu) :   42.75285       40.31350       39.07203    
    
 number of dielectric boundary points        2171
 no. dielectric boundary points in salt =            0
 no. grid points charged and not internal=           0
 iepsmp to db, and charging done at  4.9999997E-02
 number of grid points assigned charge         136
  
   setting boundary conditions
  
  some initial phi values: 
  midg,midg,1; midg,midg,igrid 
   5.2158110E-02 -3.7447758E-02
  midg,1,midg; midg,igrid,midg 
  -2.4664046E-02  2.1844592E-02
  1,midg,midg; igrid,midg,midg 
   6.5638147E-02 -7.7307217E-02
  
gauss-seidel spectral radius is        0.9980723262
  
 estimated iterations to convergence         181
   
 setup time was (sec)   7.0000000E-02
   
 now iterating at: 18:02:46
  
  
   rms-change     max change       #iterations
   1.5385315E+07   314.4564     at          10 iterations
    2696001.       131.6952     at          20 iterations
    455104.2       52.08743     at          30 iterations
    72191.55       16.35825     at          40 iterations
    12851.53       7.146667     at          50 iterations
    2102.637       2.826061     at          60 iterations
    353.9297       1.090101     at          70 iterations
    57.51370      0.4287262     at          80 iterations
    9.725001      0.1809082     at          90 iterations
    1.612670      7.6759338E-02 at         100 iterations
   0.2832688      3.2279968E-02 at         110 iterations
   4.6235479E-02  1.1840820E-02 at         120 iterations
   7.8961784E-03  5.8593750E-03 at         130 iterations
   1.3044977E-03  2.1133423E-03 at         140 iterations
   2.2178562E-04  9.2315674E-04 at         150 iterations
   3.8540249E-05  3.6621094E-04 at         160 iterations
   7.9268802E-06  2.4414063E-04 at         170 iterations
   3.3095271E-06  2.4414063E-04 at         180 iterations
   2.2838972E-06  2.4414063E-04 at         190 iterations
   2.1230474E-06  2.4414063E-04 at         200 iterations
   2.3223190E-06  2.4414063E-04 at         210 iterations
   2.3039588E-06  2.4414063E-04 at         220 iterations
   2.4603301E-06  2.4414063E-04 at         230 iterations
   2.1774604E-06  2.4414063E-04 at         240 iterations
   2.3579009E-06  2.4414063E-04 at         250 iterations
   2.1228902E-06  2.4414063E-04 at         260 iterations
   2.1574206E-06  2.4414063E-04 at         270 iterations
   2.1537187E-06  2.4414063E-04 at         280 iterations
   2.3771920E-06  2.4414063E-04 at         290 iterations
   2.0005118E-06  2.4414063E-04 at         300 iterations
   1.9808097E-06  2.4414063E-04 at         310 iterations
   2.1900439E-06  2.4414063E-04 at         320 iterations
   2.1842504E-06  2.4414063E-04 at         330 iterations
   2.1182939E-06  2.4414063E-04 at         340 iterations
   2.1802837E-06  2.4414063E-04 at         350 iterations
   2.0941029E-06  2.4414063E-04 at         360 iterations
   2.1567880E-06  2.4414063E-04 at         370 iterations
   2.2120257E-06  2.4414063E-04 at         380 iterations
   2.0990685E-06  2.4414063E-04 at         390 iterations
   2.2015711E-06  2.4414063E-04 at         400 iterations
   2.2146494E-06  2.4414063E-04 at         410 iterations
   2.1717083E-06  2.4414063E-04 at         420 iterations
   2.1642300E-06  2.4414063E-04 at         430 iterations
   2.0932239E-06  2.4414063E-04 at         440 iterations
   2.1280359E-06  2.4414063E-04 at         450 iterations
   2.0509533E-06  2.4414063E-04 at         460 iterations
   2.1489047E-06  2.4414063E-04 at         470 iterations
   2.2376050E-06  2.4414063E-04 at         480 iterations
   2.2273241E-06  2.4414063E-04 at         490 iterations
   2.3353384E-06  2.4414063E-04 at         500 iterations
   2.4922579E-06  2.4414063E-04 at         510 iterations
   2.2840768E-06  2.4414063E-04 at         520 iterations
   2.5596369E-06  2.4414063E-04 at         530 iterations
   2.2712811E-06  2.4414063E-04 at         540 iterations
   2.2807560E-06  2.4414063E-04 at         550 iterations
   2.3129803E-06  2.4414063E-04 at         560 iterations
   2.4434571E-06  2.4414063E-04 at         570 iterations
   2.2274075E-06  2.4414063E-04 at         580 iterations
   2.2864231E-06  2.4414063E-04 at         590 iterations
   2.2098448E-06  2.4414063E-04 at         600 iterations
   2.2289130E-06  2.4414063E-04 at         610 iterations
   2.3319874E-06  2.4414063E-04 at         620 iterations
   2.5804184E-06  2.4414063E-04 at         630 iterations
   2.2540464E-06  2.4414063E-04 at         640 iterations
   2.1503713E-06  2.4414063E-04 at         650 iterations
   2.0336740E-06  2.4414063E-04 at         660 iterations
   2.2734757E-06  2.4414063E-04 at         670 iterations
   2.2289782E-06  2.4414063E-04 at         680 iterations
   2.2536944E-06  2.4414063E-04 at         690 iterations
   2.1643123E-06  2.4414063E-04 at         700 iterations
   2.2050226E-06  2.4414063E-04 at         710 iterations
   2.3910266E-06  2.4414063E-04 at         720 iterations
   2.1495637E-06  2.4414063E-04 at         730 iterations
   2.2413312E-06  2.4414063E-04 at         740 iterations
   1.9968529E-06  2.4414063E-04 at         750 iterations
   2.3202388E-06  2.4414063E-04 at         760 iterations
   2.2571469E-06  2.4414063E-04 at         770 iterations
   2.0584098E-06  2.4414063E-04 at         780 iterations
   2.1339190E-06  2.4414063E-04 at         790 iterations
   2.0771981E-06  2.4414063E-04 at         800 iterations
   2.2996282E-06  2.4414063E-04 at         810 iterations
   2.1469543E-06  2.4414063E-04 at         820 iterations
   2.3267103E-06  2.4414063E-04 at         830 iterations
   2.4118665E-06  2.4414063E-04 at         840 iterations
   2.3211508E-06  2.4414063E-04 at         850 iterations
   2.2471481E-06  2.4414063E-04 at         860 iterations
   2.1486903E-06  2.4414063E-04 at         870 iterations
   2.0214170E-06  2.4414063E-04 at         880 iterations
   2.4979402E-06  2.4414063E-04 at         890 iterations
   2.1918556E-06  2.4414063E-04 at         900 iterations
   2.0684440E-06  2.4414063E-04 at         910 iterations
   1.9891415E-06  2.4414063E-04 at         920 iterations
   2.3169705E-06  2.4414063E-04 at         930 iterations
   2.3096729E-06  2.4414063E-04 at         940 iterations
   1.9081858E-06  2.4414063E-04 at         950 iterations
   2.0297730E-06  2.4414063E-04 at         960 iterations
   2.0299535E-06  2.4414063E-04 at         970 iterations
   2.3112416E-06  2.4414063E-04 at         980 iterations
   2.1600924E-06  2.4414063E-04 at         990 iterations
   2.2921042E-06  2.4414063E-04 at        1000 iterations
   2.2422535E-06  2.4414063E-04 at        1010 iterations
   2.3728601E-06  2.4414063E-04 at        1020 iterations
   2.1966016E-06  2.4414063E-04 at        1030 iterations
   2.0582213E-06  2.4414063E-04 at        1040 iterations
   2.2484519E-06  2.4414063E-04 at        1050 iterations
   2.3002522E-06  2.4414063E-04 at        1060 iterations
   2.3881935E-06  2.4414063E-04 at        1070 iterations
   2.1771859E-06  2.4414063E-04 at        1080 iterations
   2.1165524E-06  2.4414063E-04 at        1090 iterations
   2.0589191E-06  2.4414063E-04 at        1100 iterations
   2.1346416E-06  2.4414063E-04 at        1110 iterations
   2.3380535E-06  2.4414063E-04 at        1120 iterations
   2.2894867E-06  2.4414063E-04 at        1130 iterations
   2.2431393E-06  2.4414063E-04 at        1140 iterations
   2.2039180E-06  2.4414063E-04 at        1150 iterations
   2.2188390E-06  2.4414063E-04 at        1160 iterations
   2.2617201E-06  2.4414063E-04 at        1170 iterations
   2.4889084E-06  2.4414063E-04 at        1180 iterations
   2.3262910E-06  2.4414063E-04 at        1190 iterations
   2.3266700E-06  2.4414063E-04 at        1200 iterations
 finished qdiffx linear iterations
 at                       : 18:02:53
 total time elapsed so far:    6.970000    
 # loops                  :         1200
 mean,max change (kT/e)   :   2.3266700E-06  2.4414063E-04
  
 total grid energy          :        4937.821     kt
 self-reaction field energy :      1.4612769E-05 kt
 total s.charge,no epsin carrying :    0.0000
 corrected reaction field energy:   -36.36735     kt
 total reaction field energy :     -36.36734     kt
  
 coulombic energy :                -880.8419     kt
 All energy terms but grid and self_react.:  -917.2093    kt
 energy calculations done at   6.970000    
   
 writing potential map in DELPHI format
   
 potential map written to file
 fort.14                                                                         
   
   
 total cpu time was (sec)    6.970000    
   
 DelPhi exited at 18:02:53
