Mon Oct 10 14:02:35 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, 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 | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:02:35 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4426 !!! WARNING: HIT 442 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5029030 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -2.893000 67.89600 ymin,ymax (A): -12.41100 38.65000 zmin,zma (A): -20.27100 45.20400 x,y,z range (A): 70.78899 51.06100 65.47501 scale (grids/A): 0.5029030 object centre (A): 32.50150 13.11950 12.46650 number of atom coordinates read : 4426 total number of charged atoms : 4271 net assigned charge : -4.985955 assigned positive charge : 671.2889 centred at (gu) : 88.00043 89.95446 90.80249 assigned negative charge : -676.2772 centred at (gu) : 88.07167 90.07061 90.81661 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6903 nv = 96 ne = 84 npr = 92912 no. pairs analyzed = 92912 no. exposed pairs = 4994 no. arc points = 33511 no. surface atoms = 1701 nbur = 2725 mkacc time = 0.2800000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.680000 m= 247 mr = 3880 m= 0 mr = 6 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.5400000 number of dielectric boundary points 3264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3370 ## 530 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 9399 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2524838E-11 -9.5149111E-11 midg,1,midg; midg,igrid,midg 1.4970296E-10 -2.5542610E-10 1,midg,midg; igrid,midg,midg 1.2539436E-10 -1.0477576E-10 gauss-seidel spectral radius is 0.9797459 estimated iterations to convergence 58 setup time was (sec) 0.8500000 now iterating at: 14:02:38 rms-change max change #iterations 6.1104495E-02 9.358263 at 10iterations 3.6264979E-03 0.6199994 at 20iterations 4.6832513E-04 7.7739716E-02 at 30iterations 1.2101369E-04 1.5959740E-02 at 40iterations 3.4027056E-05 4.6691895E-03 at 50iterations finished qdiffx linear iterations at : 14:02:47 total time elapsed so far: 4.350000 # loops : 50 mean,max change (kT/e) : 3.4027056E-05 4.6691895E-03 energy calculations done at 4.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.530000 DelPhi exited at 14:02:48 4.531u 0.953s 0:13.05 41.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, 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 | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:02:48 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4426 !!! WARNING: HIT 442 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.508709 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -2.893000 67.89600 ymin,ymax (A): -12.41100 38.65000 zmin,zma (A): -20.27100 45.20400 x,y,z range (A): 70.78899 51.06100 65.47501 scale (grids/A): 1.508709 object centre (A): 32.50150 13.11950 12.46650 number of atom coordinates read : 4426 total number of charged atoms : 4271 net assigned charge : -4.985955 assigned positive charge : 671.2889 centred at (gu) : 83.99988 89.86234 92.40676 assigned negative charge : -676.2772 centred at (gu) : 84.21472 90.21113 92.44913 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 79284 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33511 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 23243 mr = 56854 m= 1867 mr = 16110 m= 24 mr = 817 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 1338 time to turn everything in is 0.7500000 number of dielectric boundary points 30637 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 487 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 32033 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5029030 object centre at (A) : 32.50150 13.11950 12.46650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7440008E-03 -8.4565207E-03 midg,1,midg; midg,igrid,midg 2.7629589E-03 -9.5335618E-03 1,midg,midg; igrid,midg,midg 1.5086900E-02 -6.5927473E-03 gauss-seidel spectral radius is 0.9979892 estimated iterations to convergence 177 setup time was (sec) 1.070000 now iterating at: 14:02:54 rms-change max change #iterations 3.521988 145.5962 at 10iterations 1.397872 51.42824 at 20iterations 0.5585136 18.89317 at 30iterations 0.2236780 8.458523 at 40iterations 8.9181200E-02 2.809440 at 50iterations 3.5692710E-02 1.077513 at 60iterations 1.4341866E-02 0.4565995 at 70iterations 5.8044074E-03 0.2106152 at 80iterations 2.4077741E-03 8.3885193E-02 at 90iterations 1.0353702E-03 3.6788940E-02 at 100iterations 4.8254893E-04 1.8245697E-02 at 110iterations 2.5009489E-04 8.8334084E-03 at 120iterations finished qdiffx linear iterations at : 14:03:14 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 2.5009489E-04 8.8334084E-03 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.840000 DelPhi exited at 14:03:15 9.840u 0.747s 0:26.72 39.5% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, 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 | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:03:16 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 278 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4426 !!! WARNING: HIT 442 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.263064 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -2.893000 67.89600 ymin,ymax (A): -12.41100 38.65000 zmin,zma (A): -20.27100 45.20400 x,y,z range (A): 70.78899 51.06100 65.47501 scale (grids/A): 2.263064 object centre (A): 32.50150 13.11950 12.46650 number of atom coordinates read : 4426 total number of charged atoms : 4271 net assigned charge : -4.985955 assigned positive charge : 671.2889 centred at (gu) : 80.99953 89.79311 93.60983 assigned negative charge : -676.2772 centred at (gu) : 81.32191 90.31678 93.67347 start vw surface at 0.2100000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 185172 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33511 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 84140 mr = 139012 m= 21121 mr = 67592 m= 2793 mr = 15698 m= 106 mr = 1730 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 4525 time to turn everything in is 1.760000 number of dielectric boundary points 69286 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 79 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 34067 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.508709 object centre at (A) : 32.50150 13.11950 12.46650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2110351 -0.2012534 midg,1,midg; midg,igrid,midg 3.1189166E-02 -0.1634376 1,midg,midg; igrid,midg,midg 0.3441359 -0.4680673 gauss-seidel spectral radius is 0.9991014 estimated iterations to convergence 264 setup time was (sec) 2.130000 now iterating at: 14:03:22 rms-change max change #iterations 9.487525 241.5013 at 10iterations 5.282818 128.6865 at 20iterations 2.925284 74.19608 at 30iterations 1.611982 36.50072 at 40iterations 0.8859187 18.15672 at 50iterations 0.4842439 9.336655 at 60iterations 0.2645497 4.938177 at 70iterations 0.1444937 2.903748 at 80iterations 7.8908131E-02 1.527966 at 90iterations 4.2947408E-02 0.7997513 at 100iterations 2.3389135E-02 0.4405231 at 110iterations 1.2739369E-02 0.2513885 at 120iterations 6.9478513E-03 0.1266890 at 130iterations 3.7818903E-03 7.7533960E-02 at 140iterations 2.0737415E-03 4.1655540E-02 at 150iterations 1.1435660E-03 2.4620056E-02 at 160iterations 6.3968194E-04 1.5563965E-02 at 170iterations 3.6409489E-04 7.7600479E-03 at 180iterations finished qdiffx linear iterations at : 14:03:59 total time elapsed so far: 16.52000 # loops : 180 mean,max change (kT/e) : 3.6409489E-04 7.7600479E-03 energy calculations done at 16.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.70000 DelPhi exited at 14:04:00 16.698u 2.781s 0:44.57 43.6% 0+0k 0+0io 0pf+0w