Mon Oct 10 10:21:21 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 10:21:21 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5840086 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): 19.08700 80.04500 ymin,ymax (A): 30.99900 88.93300 zmin,zma (A): -1.584000 50.38700 x,y,z range (A): 60.95800 57.93400 51.97100 scale (grids/A): 0.5840086 object centre (A): 49.56600 59.96600 24.40150 number of atom coordinates read : 2726 total number of charged atoms : 2579 net assigned charge : 6.000017 assigned positive charge : 396.8402 centred at (gu) : 87.94779 88.77499 86.90945 assigned negative charge : -390.8405 centred at (gu) : 87.83624 88.69830 86.82236 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6330 nv = 96 ne = 84 npr = 52855 no. pairs analyzed = 52855 no. exposed pairs = 4097 no. arc points = 29097 no. surface atoms = 1352 nbur = 1374 mkacc time = 0.1200000 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 = 1.456000 m= 293 mr = 2871 m= 0 mr = 17 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2830 ## 296 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7873 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0329964E-10 1.7276856E-09 midg,1,midg; midg,igrid,midg -9.4326977E-11 2.4673945E-09 1,midg,midg; igrid,midg,midg -1.4012672E-09 2.5017732E-09 gauss-seidel spectral radius is 0.9848602 estimated iterations to convergence 67 setup time was (sec) 0.5700000 now iterating at: 10:21:22 rms-change max change #iterations 9.5511965E-02 17.80328 at 10iterations 7.5155669E-03 1.270924 at 20iterations 6.0244289E-04 0.1074228 at 30iterations 5.5662604E-05 8.8500977E-03 at 40iterations 7.9715783E-06 9.6130371E-04 at 50iterations finished qdiffx linear iterations at : 10:21:24 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 7.9715783E-06 9.6130371E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 10:21:25 3.444u 0.139s 0:03.92 91.0% 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 10:21:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.752026 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): 19.08700 80.04500 ymin,ymax (A): 30.99900 88.93300 zmin,zma (A): -1.584000 50.38700 x,y,z range (A): 60.95800 57.93400 51.97100 scale (grids/A): 1.752026 object centre (A): 49.56600 59.96600 24.40150 number of atom coordinates read : 2726 total number of charged atoms : 2579 net assigned charge : 6.000017 assigned positive charge : 396.8402 centred at (gu) : 83.84303 86.32459 80.72796 assigned negative charge : -390.8405 centred at (gu) : 83.50871 86.09467 80.46679 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 68343 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29097 grid for indexing accessible points = 1.400000 m= 21575 mr = 42737 m= 2617 mr = 13997 m= 107 mr = 1178 m= 1 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 34718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 243 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 20063 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) : 0.5840086 object centre at (A) : 49.56600 59.96600 24.40150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5328299E-03 7.1659931E-03 midg,1,midg; midg,igrid,midg -1.5472716E-02 2.4127319E-02 1,midg,midg; igrid,midg,midg 2.1537344E-03 1.6443083E-02 gauss-seidel spectral radius is 0.9984162 estimated iterations to convergence 199 setup time was (sec) 0.8800000 now iterating at: 10:21:26 rms-change max change #iterations 3.550473 151.1459 at 10iterations 1.557840 56.97125 at 20iterations 0.6872606 25.24778 at 30iterations 0.3017739 10.76307 at 40iterations 0.1327626 4.686478 at 50iterations 5.8509480E-02 2.219035 at 60iterations 2.5706232E-02 0.9164520 at 70iterations 1.1373540E-02 0.4485931 at 80iterations 4.9977629E-03 0.1640816 at 90iterations 2.2008594E-03 7.6398849E-02 at 100iterations 9.7228336E-04 3.3560723E-02 at 110iterations 4.2840757E-04 1.5653610E-02 at 120iterations finished qdiffx linear iterations at : 10:21:33 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 4.2840757E-04 1.5653610E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 10:21:33 7.965u 0.194s 0:08.44 96.5% 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 10:21:33 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2726 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.628039 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): 19.08700 80.04500 ymin,ymax (A): 30.99900 88.93300 zmin,zma (A): -1.584000 50.38700 x,y,z range (A): 60.95800 57.93400 51.97100 scale (grids/A): 2.628039 object centre (A): 49.56600 59.96600 24.40150 number of atom coordinates read : 2726 total number of charged atoms : 2579 net assigned charge : 6.000017 assigned positive charge : 396.8402 centred at (gu) : 80.76434 84.48688 76.09184 assigned negative charge : -390.8405 centred at (gu) : 80.26300 84.14204 75.70028 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 158027 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29097 grid for indexing accessible points = 1.400000 m= 71713 mr = 105347 m= 22808 mr = 54316 m= 4201 mr = 16539 m= 383 mr = 2555 m= 4 mr = 177 m= 0 mr = 0 time to grow re-entrant surface = 0.7900001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.340000 number of dielectric boundary points 78202 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 20631 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) : 1.752026 object centre at (A) : 49.56600 59.96600 24.40150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6405518E-02 6.8835251E-02 midg,1,midg; midg,igrid,midg -0.5540329 0.4211386 1,midg,midg; igrid,midg,midg 5.8947511E-02 0.5004286 gauss-seidel spectral radius is 0.9992157 estimated iterations to convergence 282 setup time was (sec) 1.710000 now iterating at: 10:21:35 rms-change max change #iterations 9.121521 283.1489 at 10iterations 5.375084 150.6266 at 20iterations 3.118319 89.16470 at 30iterations 1.805617 50.64516 at 40iterations 1.034403 27.31734 at 50iterations 0.5903320 16.18905 at 60iterations 0.3369662 8.177612 at 70iterations 0.1918116 4.594878 at 80iterations 0.1090825 2.642857 at 90iterations 6.1945274E-02 1.563408 at 100iterations 3.5084669E-02 0.9287033 at 110iterations 1.9859485E-02 0.4591312 at 120iterations 1.1262316E-02 0.2319498 at 130iterations 6.3861152E-03 0.1297493 at 140iterations 3.6057846E-03 7.6017380E-02 at 150iterations 2.0405515E-03 4.1989803E-02 at 160iterations 1.1537892E-03 3.1366348E-02 at 170iterations 6.5482268E-04 1.3082504E-02 at 180iterations finished qdiffx linear iterations at : 10:21:46 total time elapsed so far: 12.82000 # loops : 180 mean,max change (kT/e) : 6.5482268E-04 1.3082504E-02 energy calculations done at 12.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.02000 DelPhi exited at 10:21:47 13.021u 0.228s 0:13.54 97.7% 0+0k 0+0io 0pf+0w