Mon Oct 10 16:32:15 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 16:32:15 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 = 2309 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6357483 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): 29.76600 85.76300 ymin,ymax (A): 28.84800 76.46900 zmin,zma (A): -27.94600 21.48900 x,y,z range (A): 55.99700 47.62100 49.43500 scale (grids/A): 0.6357483 object centre (A): 57.76450 52.65850 -3.228499 number of atom coordinates read : 2309 total number of charged atoms : 2232 net assigned charge : -0.9999951 assigned positive charge : 341.0502 centred at (gu) : 89.05933 91.02274 90.11885 assigned negative charge : -342.0509 centred at (gu) : 89.20684 91.05314 90.11438 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6232 nv = 96 ne = 84 npr = 46061 no. pairs analyzed = 46061 no. exposed pairs = 3154 no. arc points = 22350 no. surface atoms = 1063 nbur = 1246 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 396 mr = 3095 m= 4 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3494 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2191 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7685 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7498050E-09 -1.0014426E-09 midg,1,midg; midg,igrid,midg 1.0935366E-09 -5.2106275E-09 1,midg,midg; igrid,midg,midg 1.4634407E-08 -1.2292840E-08 gauss-seidel spectral radius is 0.9871655 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 16:32:15 rms-change max change #iterations 0.1285473 24.64361 at 10iterations 1.2399544E-02 2.529123 at 20iterations 1.1914228E-03 0.1799259 at 30iterations 1.1832012E-04 1.8484116E-02 at 40iterations 1.1880712E-05 2.0051003E-03 at 50iterations finished qdiffx linear iterations at : 16:32:18 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.1880712E-05 2.0051003E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 16:32:19 3.407u 0.180s 0:03.93 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 16:32:19 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 = 2309 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.907245 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): 29.76600 85.76300 ymin,ymax (A): 28.84800 76.46900 zmin,zma (A): -27.94600 21.48900 x,y,z range (A): 55.99700 47.62100 49.43500 scale (grids/A): 1.907245 object centre (A): 57.76450 52.65850 -3.228499 number of atom coordinates read : 2309 total number of charged atoms : 2232 net assigned charge : -0.9999951 assigned positive charge : 341.0502 centred at (gu) : 87.17754 93.06819 90.35616 assigned negative charge : -342.0509 centred at (gu) : 87.62043 93.15932 90.34296 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 66276 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22350 grid for indexing accessible points = 1.400000 m= 23913 mr = 43258 m= 4558 mr = 16834 m= 342 mr = 2761 m= 2 mr = 126 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 32112 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17591 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) : 0.6357483 object centre at (A) : 57.76450 52.65850 -3.228499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8926952E-02 -5.6096388E-04 midg,1,midg; midg,igrid,midg 6.5272569E-04 -3.5451695E-02 1,midg,midg; igrid,midg,midg 7.9472363E-02 -7.5987023E-03 gauss-seidel spectral radius is 0.9986237 estimated iterations to convergence 214 setup time was (sec) 0.5700000 now iterating at: 16:32:20 rms-change max change #iterations 3.956675 193.6934 at 10iterations 1.835029 75.07008 at 20iterations 0.8560258 32.32293 at 30iterations 0.3995613 13.25894 at 40iterations 0.1867699 6.053186 at 50iterations 8.6969674E-02 3.172162 at 60iterations 4.0541127E-02 1.393948 at 70iterations 1.8955935E-02 0.6500670 at 80iterations 8.8405618E-03 0.3275900 at 90iterations 4.1293181E-03 0.1446619 at 100iterations 1.9229233E-03 6.2139511E-02 at 110iterations 9.0194825E-04 2.8652191E-02 at 120iterations finished qdiffx linear iterations at : 16:32:27 total time elapsed so far: 7.720000 # loops : 120 mean,max change (kT/e) : 9.0194825E-04 2.8652191E-02 energy calculations done at 7.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.860000 DelPhi exited at 16:32:27 7.861u 0.195s 0:08.58 93.8% 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 16:32:28 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 = 2309 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.860868 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): 29.76600 85.76300 ymin,ymax (A): 28.84800 76.46900 zmin,zma (A): -27.94600 21.48900 x,y,z range (A): 55.99700 47.62100 49.43500 scale (grids/A): 2.860868 object centre (A): 57.76450 52.65850 -3.228499 number of atom coordinates read : 2309 total number of charged atoms : 2232 net assigned charge : -0.9999951 assigned positive charge : 341.0502 centred at (gu) : 85.76605 94.60201 90.53413 assigned negative charge : -342.0509 centred at (gu) : 86.43060 94.73888 90.51450 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 153186 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22350 grid for indexing accessible points = 1.400000 m= 74930 mr = 105907 m= 29434 mr = 59058 m= 8401 mr = 22918 m= 1372 mr = 6223 m= 79 mr = 870 m= 0 mr = 36 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8900000 number of dielectric boundary points 72390 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 17856 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) : 1.907245 object centre at (A) : 57.76450 52.65850 -3.228499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3633022 6.1754763E-02 midg,1,midg; midg,igrid,midg 1.4554062E-02 -0.4251864 1,midg,midg; igrid,midg,midg 1.277033 -7.5080246E-02 gauss-seidel spectral radius is 0.9992603 estimated iterations to convergence 290 setup time was (sec) 1.110000 now iterating at: 16:32:29 rms-change max change #iterations 9.454284 370.1710 at 10iterations 5.591817 181.6087 at 20iterations 3.270673 74.46754 at 30iterations 1.914689 43.51213 at 40iterations 1.111440 22.00220 at 50iterations 0.6461995 13.56858 at 60iterations 0.3738097 8.080917 at 70iterations 0.2161110 4.079544 at 80iterations 0.1249853 2.626724 at 90iterations 7.1922578E-02 1.450706 at 100iterations 4.1284166E-02 0.7890677 at 110iterations 2.3837494E-02 0.4835281 at 120iterations 1.3698259E-02 0.2654264 at 130iterations 7.8607276E-03 0.1562881 at 140iterations 4.5226808E-03 8.5172653E-02 at 150iterations 2.6008282E-03 4.8334718E-02 at 160iterations 1.4951573E-03 2.7893066E-02 at 170iterations 8.5890316E-04 1.6172409E-02 at 180iterations finished qdiffx linear iterations at : 16:32:40 total time elapsed so far: 12.38000 # loops : 180 mean,max change (kT/e) : 8.5890316E-04 1.6172409E-02 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 16:32:41 12.508u 0.222s 0:13.05 97.4% 0+0k 0+0io 0pf+0w