Tue Oct 11 01:59:16 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 Tue Oct 11 2011 at 01:59:17 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5716029 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): 8.241000 70.52200 ymin,ymax (A): -10.87600 39.54000 zmin,zma (A): 35.11200 77.07200 x,y,z range (A): 62.28100 50.41600 41.96000 scale (grids/A): 0.5716029 object centre (A): 39.38150 14.33200 56.09200 number of atom coordinates read : 2570 total number of charged atoms : 2422 net assigned charge : 6.812018 assigned positive charge : 384.3518 centred at (gu) : 92.19152 90.58324 90.08193 assigned negative charge : -377.5405 centred at (gu) : 92.01679 90.68526 89.92003 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5404 nv = 96 ne = 84 npr = 51985 no. pairs analyzed = 51985 no. exposed pairs = 3036 no. arc points = 21420 no. surface atoms = 1036 nbur = 1534 mkacc time = 9.0000004E-02 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 = 1.512000 m= 225 mr = 2933 m= 0 mr = 12 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2000000 number of dielectric boundary points 2684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2172 ## 259 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 6960 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2373811E-09 3.3437069E-09 midg,1,midg; midg,igrid,midg 2.1495319E-09 -4.6528700E-10 1,midg,midg; igrid,midg,midg -8.4277746E-10 5.8528387E-09 gauss-seidel spectral radius is 0.9841694 estimated iterations to convergence 65 setup time was (sec) 0.3800000 now iterating at: 01:59:17 rms-change max change #iterations 8.4872596E-02 17.77648 at 10iterations 7.3958263E-03 1.228973 at 20iterations 9.8259770E-04 0.2345352 at 30iterations 2.2501482E-04 6.0707092E-02 at 40iterations 5.8483314E-05 1.5773773E-02 at 50iterations finished qdiffx linear iterations at : 01:59:20 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 5.8483314E-05 1.5773773E-02 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 01:59:21 3.392u 0.189s 0:04.28 83.4% 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 Tue Oct 11 2011 at 01:59:21 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.714809 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): 8.241000 70.52200 ymin,ymax (A): -10.87600 39.54000 zmin,zma (A): 35.11200 77.07200 x,y,z range (A): 62.28100 50.41600 41.96000 scale (grids/A): 1.714809 object centre (A): 39.38150 14.33200 56.09200 number of atom coordinates read : 2570 total number of charged atoms : 2422 net assigned charge : 6.812018 assigned positive charge : 384.3518 centred at (gu) : 96.57415 91.74901 90.24547 assigned negative charge : -377.5405 centred at (gu) : 96.05007 92.05566 89.75986 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 59856 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21420 grid for indexing accessible points = 1.400000 m= 19263 mr = 41415 m= 2289 mr = 13885 m= 68 mr = 1316 m= 0 mr = 2 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 572 time to turn everything in is 0.3000000 number of dielectric boundary points 24858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 218 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 18743 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) : 0.5716029 object centre at (A) : 39.38150 14.33200 56.09200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8144443E-03 1.8020995E-02 midg,1,midg; midg,igrid,midg 1.3230612E-02 7.4099842E-03 1,midg,midg; igrid,midg,midg 6.3668191E-03 -2.7408337E-04 gauss-seidel spectral radius is 0.9983096 estimated iterations to convergence 193 setup time was (sec) 0.5100000 now iterating at: 01:59:22 rms-change max change #iterations 3.368796 157.2623 at 10iterations 1.447208 61.63846 at 20iterations 0.6211703 21.46247 at 30iterations 0.2681603 10.00522 at 40iterations 0.1159664 4.018700 at 50iterations 5.0225373E-02 1.729126 at 60iterations 2.1708859E-02 0.8413696 at 70iterations 9.4462959E-03 0.3498650 at 80iterations 4.2421706E-03 0.1698933 at 90iterations 1.9550505E-03 7.9353333E-02 at 100iterations 9.4412721E-04 4.0431976E-02 at 110iterations 4.9298571E-04 2.5196075E-02 at 120iterations finished qdiffx linear iterations at : 01:59:29 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 4.9298571E-04 2.5196075E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 01:59:29 7.651u 0.189s 0:08.40 93.2% 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 Tue Oct 11 2011 at 01:59:29 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2570 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.572213 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): 8.241000 70.52200 ymin,ymax (A): -10.87600 39.54000 zmin,zma (A): 35.11200 77.07200 x,y,z range (A): 62.28100 50.41600 41.96000 scale (grids/A): 2.572213 object centre (A): 39.38150 14.33200 56.09200 number of atom coordinates read : 2570 total number of charged atoms : 2422 net assigned charge : 6.812018 assigned positive charge : 384.3518 centred at (gu) : 99.86105 92.62341 90.36784 assigned negative charge : -377.5405 centred at (gu) : 99.07509 93.08352 89.63979 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 138982 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21420 grid for indexing accessible points = 1.400000 m= 65586 mr = 100872 m= 20376 mr = 53207 m= 3696 mr = 16067 m= 270 mr = 2627 m= 4 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 1827 time to turn everything in is 0.7300000 number of dielectric boundary points 56027 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 19363 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) : 1.714809 object centre at (A) : 39.38150 14.33200 56.09200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8190011E-02 0.2247044 midg,1,midg; midg,igrid,midg 0.1509791 0.1467529 1,midg,midg; igrid,midg,midg 0.1537904 -0.2130020 gauss-seidel spectral radius is 0.9991616 estimated iterations to convergence 273 setup time was (sec) 0.9600000 now iterating at: 01:59:31 rms-change max change #iterations 8.335697 323.1202 at 10iterations 4.639898 101.6664 at 20iterations 2.585021 55.57475 at 30iterations 1.436916 32.13456 at 40iterations 0.7968618 17.46951 at 50iterations 0.4426941 10.03096 at 60iterations 0.2451926 4.905975 at 70iterations 0.1357633 2.809921 at 80iterations 7.5370058E-02 1.820469 at 90iterations 4.1915786E-02 0.8499649 at 100iterations 2.3243111E-02 0.4859295 at 110iterations 1.2945084E-02 0.2694550 at 120iterations 7.2396952E-03 0.1677742 at 130iterations 4.1050315E-03 9.6382141E-02 at 140iterations 2.3533558E-03 5.6346893E-02 at 150iterations 1.3898469E-03 3.5942078E-02 at 160iterations 8.4852276E-04 2.5859833E-02 at 170iterations 5.4628926E-04 1.6742706E-02 at 180iterations finished qdiffx linear iterations at : 01:59:41 total time elapsed so far: 11.92000 # loops : 180 mean,max change (kT/e) : 5.4628926E-04 1.6742706E-02 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.06000 DelPhi exited at 01:59:42 12.059u 0.194s 0:12.54 97.6% 0+0k 0+0io 0pf+0w