Mon Oct 10 17:01:47 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+sph.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 = amb.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 17:01:47 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 = 4588 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5242310 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): -24.04300 40.06600 ymin,ymax (A): -18.05700 47.19500 zmin,zma (A): 7.120000 75.02900 x,y,z range (A): 64.10900 65.25200 67.90900 scale (grids/A): 0.5242310 object centre (A): 8.011501 14.56900 41.07450 number of atom coordinates read : 4588 total number of charged atoms : 4349 net assigned charge : 7.800026 assigned positive charge : 693.8467 centred at (gu) : 91.28800 88.49236 87.52992 assigned negative charge : -686.0505 centred at (gu) : 91.39571 88.60706 87.38263 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8054 nv = 96 ne = 84 npr = 91458 no. pairs analyzed = 91458 no. exposed pairs = 6062 no. arc points = 41694 no. surface atoms = 2024 nbur = 2564 mkacc time = 0.2000000 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 = 1.624000 m= 311 mr = 4037 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4321 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4043 ## 545 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 10610 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5105573E-10 4.4839910E-10 midg,1,midg; midg,igrid,midg 1.0425946E-09 -1.9369255E-10 1,midg,midg; igrid,midg,midg 4.8551119E-10 -3.6719688E-10 gauss-seidel spectral radius is 0.9813780 estimated iterations to convergence 60 setup time was (sec) 0.7000000 now iterating at: 17:01:48 rms-change max change #iterations 7.3952526E-02 11.31328 at 10iterations 4.9118176E-03 0.7166748 at 20iterations 8.2349998E-04 0.1223240 at 30iterations 3.2183831E-04 5.4571152E-02 at 40iterations 1.3723594E-04 2.4085999E-02 at 50iterations finished qdiffx linear iterations at : 17:01:51 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 1.3723594E-04 2.4085999E-02 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 17:01:52 3.518u 0.161s 0:04.90 74.8% 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 17:01:52 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 = 4588 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.572693 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): -24.04300 40.06600 ymin,ymax (A): -18.05700 47.19500 zmin,zma (A): 7.120000 75.02900 x,y,z range (A): 64.10900 65.25200 67.90900 scale (grids/A): 1.572693 object centre (A): 8.011501 14.56900 41.07450 number of atom coordinates read : 4588 total number of charged atoms : 4349 net assigned charge : 7.800026 assigned positive charge : 693.8467 centred at (gu) : 93.86211 85.47578 82.58833 assigned negative charge : -686.0505 centred at (gu) : 94.18679 85.82088 82.14747 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 90824 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41694 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 26912 mr = 61314 m= 2558 mr = 17774 m= 71 mr = 1054 m= 0 mr = 4 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 40219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 489 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 32948 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) : 0.5242310 object centre at (A) : 8.011501 14.56900 41.07450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3332133E-03 2.4160895E-02 midg,1,midg; midg,igrid,midg 7.9687452E-03 -9.5511274E-03 1,midg,midg; igrid,midg,midg 1.4800008E-02 2.0304748E-03 gauss-seidel spectral radius is 0.9982039 estimated iterations to convergence 187 setup time was (sec) 0.9300000 now iterating at: 17:01:54 rms-change max change #iterations 3.950380 166.3132 at 10iterations 1.651892 66.11591 at 20iterations 0.6936817 25.59731 at 30iterations 0.2901447 9.869583 at 40iterations 0.1219424 4.173538 at 50iterations 5.1344939E-02 1.658546 at 60iterations 2.1581518E-02 0.7081814 at 70iterations 9.2080506E-03 0.3177083 at 80iterations 4.0127845E-03 0.1358628 at 90iterations 1.8669448E-03 6.1182022E-02 at 100iterations 9.7141991E-04 3.3827782E-02 at 110iterations 5.8948464E-04 2.1476746E-02 at 120iterations finished qdiffx linear iterations at : 17:02:00 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 5.8948464E-04 2.1476746E-02 energy calculations done at 7.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.350000 DelPhi exited at 17:02:01 7.353u 0.212s 0:08.56 88.3% 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 17:02:01 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 = 4588 !!! WARNING: HEM 810 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.359039 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): -24.04300 40.06600 ymin,ymax (A): -18.05700 47.19500 zmin,zma (A): 7.120000 75.02900 x,y,z range (A): 64.10900 65.25200 67.90900 scale (grids/A): 2.359039 object centre (A): 8.011501 14.56900 41.07450 number of atom coordinates read : 4588 total number of charged atoms : 4349 net assigned charge : 7.800026 assigned positive charge : 693.8467 centred at (gu) : 95.79295 83.21312 78.88218 assigned negative charge : -686.0505 centred at (gu) : 96.28013 83.73121 78.22113 start vw surface at 0.2200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 211587 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41694 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 95949 mr = 151454 m= 25133 mr = 74260 m= 3744 mr = 17848 m= 214 mr = 2163 m= 3 mr = 80 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 90826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 45 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 34732 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) : 1.572693 object centre at (A) : 8.011501 14.56900 41.07450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4768126 0.4935698 midg,1,midg; midg,igrid,midg 8.7276965E-02 -0.2054714 1,midg,midg; igrid,midg,midg 0.2830028 5.9740704E-02 gauss-seidel spectral radius is 0.9991866 estimated iterations to convergence 277 setup time was (sec) 1.860000 now iterating at: 17:02:03 rms-change max change #iterations 10.47807 358.3701 at 10iterations 6.039010 144.9621 at 20iterations 3.457620 80.62394 at 30iterations 1.968329 40.24805 at 40iterations 1.119191 25.80380 at 50iterations 0.6324669 12.00892 at 60iterations 0.3570721 7.382912 at 70iterations 0.2014804 4.932868 at 80iterations 0.1133258 2.115292 at 90iterations 6.3782871E-02 1.290612 at 100iterations 3.5862498E-02 0.8286133 at 110iterations 2.0142928E-02 0.3981876 at 120iterations 1.1294209E-02 0.2450638 at 130iterations 6.3437587E-03 0.1271439 at 140iterations 3.5542082E-03 7.7339172E-02 at 150iterations 1.9895060E-03 3.5105467E-02 at 160iterations 1.1186560E-03 2.1206379E-02 at 170iterations 6.2733778E-04 1.3277054E-02 at 180iterations finished qdiffx linear iterations at : 17:02:13 total time elapsed so far: 11.98000 # loops : 180 mean,max change (kT/e) : 6.2733778E-04 1.3277054E-02 energy calculations done at 11.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.16000 DelPhi exited at 17:02:14 12.162u 0.235s 0:12.80 96.7% 0+0k 0+0io 0pf+0w