Tue Oct 11 08:17:05 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 08:17:05 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3621 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HIZ 170 has a net charge of 0.2000 !!! WARNING: HIZ 273 has a net charge of 0.2000 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: HIZ 682 has a net charge of 0.2000 !!! WARNING: HIZ 784 has a net charge of 0.2000 !!! WARNING: ZN1 1025 has a net charge of 1.4000 !!! WARNING: ZN1 1026 has a net charge of 1.4000 !!! WARNING: ZN1 1027 has a net charge of 1.4000 !!! WARNING: ZN1 1031 has a net charge of 1.4000 !!! WARNING: ZN1 1032 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.4974707 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): -53.38400 -0.1880001 ymin,ymax (A): -38.38800 21.58600 zmin,zma (A): 11.19900 82.76100 x,y,z range (A): 53.19600 59.97400 71.56200 scale (grids/A): 0.4974707 object centre (A): -26.78600 -8.401000 46.98000 number of atom coordinates read : 3621 total number of charged atoms : 3450 net assigned charge : 7.920008 assigned positive charge : 553.6450 centred at (gu) : 88.18036 90.11014 91.36772 assigned negative charge : -545.7266 centred at (gu) : 88.35635 90.14635 91.35490 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 5684 nv = 96 ne = 84 npr = 69292 no. pairs analyzed = 69292 no. exposed pairs = 5392 no. arc points = 38910 no. surface atoms = 1775 nbur = 1846 mkacc time = 0.2300000 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 = 1.708000 m= 197 mr = 2353 m= 1 mr = 0 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 0.5000000 number of dielectric boundary points 3529 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3761 ## 659 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 7797 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0336230E-11 1.0281766E-10 midg,1,midg; midg,igrid,midg 9.4369429E-11 1.7372008E-11 1,midg,midg; igrid,midg,midg 4.0765719E-10 -8.6153432E-11 gauss-seidel spectral radius is 0.9792769 estimated iterations to convergence 57 setup time was (sec) 0.7800000 now iterating at: 08:17:06 rms-change max change #iterations 5.5788238E-02 10.13565 at 10iterations 2.8786573E-03 0.4748917 at 20iterations 1.7429692E-04 3.0197144E-02 at 30iterations 2.0267917E-05 2.6454926E-03 at 40iterations 3.4092207E-06 3.5476685E-04 at 50iterations finished qdiffx linear iterations at : 08:17:10 total time elapsed so far: 4.550000 # loops : 50 mean,max change (kT/e) : 3.4092207E-06 3.5476685E-04 energy calculations done at 4.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.780000 DelPhi exited at 08:17:11 4.787u 0.406s 0:05.55 93.3% 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 Tue Oct 11 2011 at 08:17:11 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3621 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HIZ 170 has a net charge of 0.2000 !!! WARNING: HIZ 273 has a net charge of 0.2000 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: HIZ 682 has a net charge of 0.2000 !!! WARNING: HIZ 784 has a net charge of 0.2000 !!! WARNING: ZN1 1025 has a net charge of 1.4000 !!! WARNING: ZN1 1026 has a net charge of 1.4000 !!! WARNING: ZN1 1027 has a net charge of 1.4000 !!! WARNING: ZN1 1031 has a net charge of 1.4000 !!! WARNING: ZN1 1032 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.492412 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): -53.38400 -0.1880001 ymin,ymax (A): -38.38800 21.58600 zmin,zma (A): 11.19900 82.76100 x,y,z range (A): 53.19600 59.97400 71.56200 scale (grids/A): 1.492412 object centre (A): -26.78600 -8.401000 46.98000 number of atom coordinates read : 3621 total number of charged atoms : 3450 net assigned charge : 7.920008 assigned positive charge : 553.6450 centred at (gu) : 84.54018 90.32976 94.10226 assigned negative charge : -545.7266 centred at (gu) : 85.06873 90.43856 94.06416 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 64012 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38910 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 15318 mr = 38570 m= 1027 mr = 8458 m= 19 mr = 235 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 99 time to turn everything in is 0.6800000 number of dielectric boundary points 33113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 560 ## 11 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 25687 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) : 0.4974707 object centre at (A) : -26.78600 -8.401000 46.98000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2622850E-03 1.6700685E-02 midg,1,midg; midg,igrid,midg 1.1811564E-03 -6.4467713E-03 1,midg,midg; igrid,midg,midg 1.2606774E-02 -1.7299011E-03 gauss-seidel spectral radius is 0.9978963 estimated iterations to convergence 173 setup time was (sec) 1.040000 now iterating at: 08:17:12 rms-change max change #iterations 3.078165 166.4481 at 10iterations 1.185453 46.25531 at 20iterations 0.4622769 17.93485 at 30iterations 0.1788787 7.259457 at 40iterations 6.9254063E-02 2.840116 at 50iterations 2.6900925E-02 1.081945 at 60iterations 1.0394723E-02 0.4273834 at 70iterations 4.0648491E-03 0.1600266 at 80iterations 1.5836307E-03 6.2614441E-02 at 90iterations 6.1623694E-04 2.3418427E-02 at 100iterations 2.4092538E-04 1.0168076E-02 at 110iterations 9.4406772E-05 3.4790039E-03 at 120iterations finished qdiffx linear iterations at : 08:17:21 total time elapsed so far: 10.32000 # loops : 120 mean,max change (kT/e) : 9.4406772E-05 3.4790039E-03 energy calculations done at 10.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.54000 DelPhi exited at 08:17:22 10.543u 0.462s 0:11.32 97.1% 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 08:17:22 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3621 !!! WARNING: HIZ 67 has a net charge of 0.2000 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HIZ 170 has a net charge of 0.2000 !!! WARNING: HIZ 273 has a net charge of 0.2000 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: HIZ 682 has a net charge of 0.2000 !!! WARNING: HIZ 784 has a net charge of 0.2000 !!! WARNING: ZN1 1025 has a net charge of 1.4000 !!! WARNING: ZN1 1026 has a net charge of 1.4000 !!! WARNING: ZN1 1027 has a net charge of 1.4000 !!! WARNING: ZN1 1031 has a net charge of 1.4000 !!! WARNING: ZN1 1032 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= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.238618 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): -53.38400 -0.1880001 ymin,ymax (A): -38.38800 21.58600 zmin,zma (A): 11.19900 82.76100 x,y,z range (A): 53.19600 59.97400 71.56200 scale (grids/A): 2.238618 object centre (A): -26.78600 -8.401000 46.98000 number of atom coordinates read : 3621 total number of charged atoms : 3450 net assigned charge : 7.920008 assigned positive charge : 553.6450 centred at (gu) : 81.80994 90.49425 96.15301 assigned negative charge : -545.7266 centred at (gu) : 82.60297 90.65767 96.09613 start vw surface at 0.1900000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 149325 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38910 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 56985 mr = 96611 m= 11520 mr = 40166 m= 1166 mr = 6790 m= 49 mr = 440 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 359 time to turn everything in is 1.620000 number of dielectric boundary points 75033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 1.770000 number of grid points assigned charge 27527 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) : 1.492412 object centre at (A) : -26.78600 -8.401000 46.98000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4485041E-04 0.1964256 midg,1,midg; midg,igrid,midg 1.8826231E-02 -0.1811707 1,midg,midg; igrid,midg,midg 0.1978783 -2.1642683E-02 gauss-seidel spectral radius is 0.9990702 estimated iterations to convergence 259 setup time was (sec) 1.980000 now iterating at: 08:17:24 rms-change max change #iterations 8.665713 276.8474 at 10iterations 4.895495 125.4047 at 20iterations 2.714536 72.68845 at 30iterations 1.494187 37.52175 at 40iterations 0.8186713 21.01753 at 50iterations 0.4453622 10.61798 at 60iterations 0.2420961 5.534630 at 70iterations 0.1310424 3.663649 at 80iterations 7.0734821E-02 1.771002 at 90iterations 3.8165536E-02 0.9394684 at 100iterations 2.0602178E-02 0.4854463 at 110iterations 1.1054805E-02 0.2567348 at 120iterations 5.9328112E-03 0.1466103 at 130iterations 3.2004835E-03 7.3110580E-02 at 140iterations 1.7153500E-03 4.0557861E-02 at 150iterations 9.1922446E-04 2.0837784E-02 at 160iterations 4.9383997E-04 1.1070251E-02 at 170iterations 2.6534707E-04 5.9595108E-03 at 180iterations finished qdiffx linear iterations at : 08:17:40 total time elapsed so far: 17.18000 # loops : 180 mean,max change (kT/e) : 2.6534707E-04 5.9595108E-03 energy calculations done at 17.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.40000 DelPhi exited at 08:17:40 17.408u 0.483s 0:18.26 97.9% 0+0k 0+0io 0pf+0w