Mon Oct 10 14:16:32 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 14:16:32 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 = 2605 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: 0.6407141 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): -12.39500 39.43700 ymin,ymax (A): -23.88300 24.26600 zmin,zma (A): -0.4430000 55.12000 x,y,z range (A): 51.83200 48.14900 55.56300 scale (grids/A): 0.6407141 object centre (A): 13.52100 0.1914988 27.33850 number of atom coordinates read : 2605 total number of charged atoms : 2461 net assigned charge : 5.500007 assigned positive charge : 399.0496 centred at (gu) : 90.45798 90.15872 91.03963 assigned negative charge : -393.5503 centred at (gu) : 90.40955 90.00186 91.15647 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7174 nv = 96 ne = 84 npr = 50862 no. pairs analyzed = 50862 no. exposed pairs = 3389 no. arc points = 23750 no. surface atoms = 1145 nbur = 1460 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 367 mr = 3765 m= 5 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2474 ## 281 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8621 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7796070E-08 -7.6263058E-09 midg,1,midg; midg,igrid,midg -1.0546355E-08 2.7801148E-08 1,midg,midg; igrid,midg,midg 2.2370739E-09 1.5530745E-08 gauss-seidel spectral radius is 0.9873824 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 14:16:33 rms-change max change #iterations 0.1460991 20.70727 at 10iterations 1.5154796E-02 2.503141 at 20iterations 2.0015731E-03 0.3698235 at 30iterations 4.5788230E-04 7.6747894E-02 at 40iterations 1.3784309E-04 2.2529602E-02 at 50iterations finished qdiffx linear iterations at : 14:16:36 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 1.3784309E-04 2.2529602E-02 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 14:16:36 3.225u 0.141s 0:03.87 86.8% 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 14:16:36 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 = 2605 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: 1.922142 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): -12.39500 39.43700 ymin,ymax (A): -23.88300 24.26600 zmin,zma (A): -0.4430000 55.12000 x,y,z range (A): 51.83200 48.14900 55.56300 scale (grids/A): 1.922142 object centre (A): 13.52100 0.1914988 27.33850 number of atom coordinates read : 2605 total number of charged atoms : 2461 net assigned charge : 5.500007 assigned positive charge : 399.0496 centred at (gu) : 91.37339 90.47556 93.11815 assigned negative charge : -393.5503 centred at (gu) : 91.22816 90.00514 93.46936 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77484 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23750 grid for indexing accessible points = 1.400000 m= 26975 mr = 52613 m= 3968 mr = 19086 m= 256 mr = 2224 m= 7 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 34662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 195 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19343 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) : 0.6407141 object centre at (A) : 13.52100 0.1914988 27.33850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8203986E-02 8.1675649E-03 midg,1,midg; midg,igrid,midg -2.7849762E-02 1.8847894E-02 1,midg,midg; igrid,midg,midg 1.1602649E-02 2.5115300E-03 gauss-seidel spectral radius is 0.9986686 estimated iterations to convergence 217 setup time was (sec) 0.8500000 now iterating at: 14:16:37 rms-change max change #iterations 4.351380 183.5597 at 10iterations 2.061104 73.66747 at 20iterations 0.9721784 30.32111 at 30iterations 0.4609158 14.57079 at 40iterations 0.2175777 6.544474 at 50iterations 0.1028018 3.661826 at 60iterations 4.8726171E-02 1.528111 at 70iterations 2.3137940E-02 0.7159572 at 80iterations 1.1116800E-02 0.3475115 at 90iterations 5.4002698E-03 0.1690292 at 100iterations 2.6815515E-03 9.1623306E-02 at 110iterations 1.3853426E-03 5.2047729E-02 at 120iterations finished qdiffx linear iterations at : 14:16:44 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 1.3853426E-03 5.2047729E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 14:16:45 8.043u 0.259s 0:08.74 94.8% 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 14:16:45 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 = 2605 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.883214 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): -12.39500 39.43700 ymin,ymax (A): -23.88300 24.26600 zmin,zma (A): -0.4430000 55.12000 x,y,z range (A): 51.83200 48.14900 55.56300 scale (grids/A): 2.883214 object centre (A): 13.52100 0.1914988 27.33850 number of atom coordinates read : 2605 total number of charged atoms : 2461 net assigned charge : 5.500007 assigned positive charge : 399.0496 centred at (gu) : 92.05986 90.71312 94.67716 assigned negative charge : -393.5503 centred at (gu) : 91.84216 90.00777 95.20372 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 179361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23750 grid for indexing accessible points = 1.400000 m= 88619 mr = 128184 m= 30035 mr = 71059 m= 6735 mr = 23134 m= 1128 mr = 4669 m= 74 mr = 772 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.410000 number of dielectric boundary points 78118 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 19688 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) : 1.922142 object centre at (A) : 13.52100 0.1914988 27.33850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5451377 -0.1076239 midg,1,midg; midg,igrid,midg -0.3732234 0.2118671 1,midg,midg; igrid,midg,midg 0.2163753 2.9528695E-03 gauss-seidel spectral radius is 0.9992721 estimated iterations to convergence 292 setup time was (sec) 1.740000 now iterating at: 14:16:47 rms-change max change #iterations 10.35908 422.8817 at 10iterations 6.162828 156.2686 at 20iterations 3.636587 71.12959 at 30iterations 2.132009 42.53862 at 40iterations 1.245898 24.78773 at 50iterations 0.7290651 13.99998 at 60iterations 0.4248872 7.439451 at 70iterations 0.2470657 4.671484 at 80iterations 0.1436381 2.779240 at 90iterations 8.3345748E-02 1.666561 at 100iterations 4.8411850E-02 0.8452721 at 110iterations 2.8193079E-02 0.4947472 at 120iterations 1.6455537E-02 0.3113289 at 130iterations 9.6854055E-03 0.1773529 at 140iterations 5.7596657E-03 0.1040344 at 150iterations 3.5011002E-03 7.0251465E-02 at 160iterations 2.2120485E-03 4.5124054E-02 at 170iterations 1.4696165E-03 3.3058167E-02 at 180iterations finished qdiffx linear iterations at : 14:16:59 total time elapsed so far: 13.99000 # loops : 180 mean,max change (kT/e) : 1.4696165E-03 3.3058167E-02 energy calculations done at 13.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.16000 DelPhi exited at 14:17:00 14.164u 0.282s 0:14.89 96.9% 0+0k 0+0io 0pf+0w