Sat Oct 8 11:51:37 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 Sat Oct 8 2011 at 11:51:38 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 = 2492 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: 0.6367034 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): -24.59100 31.32200 ymin,ymax (A): -6.031000 40.33500 zmin,zma (A): 8.618000 50.86600 x,y,z range (A): 55.91300 46.36600 42.24800 scale (grids/A): 0.6367034 object centre (A): 3.365500 17.15200 29.74200 number of atom coordinates read : 2492 total number of charged atoms : 2352 net assigned charge : -1.999994 assigned positive charge : 378.3742 centred at (gu) : 89.90433 89.70210 90.88035 assigned negative charge : -380.3746 centred at (gu) : 90.02061 89.56741 90.88886 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6698 nv = 96 ne = 84 npr = 51055 no. pairs analyzed = 51055 no. exposed pairs = 2955 no. arc points = 21567 no. surface atoms = 1002 nbur = 1490 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 348 mr = 3658 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3400000 number of dielectric boundary points 3353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2122 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8113 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4230456E-09 -4.1860382E-09 midg,1,midg; midg,igrid,midg -1.7989546E-08 1.0552780E-08 1,midg,midg; igrid,midg,midg 9.6056345E-09 -1.4577117E-08 gauss-seidel spectral radius is 0.9872105 estimated iterations to convergence 72 setup time was (sec) 0.6100000 now iterating at: 11:51:38 rms-change max change #iterations 0.1414089 21.51369 at 10iterations 1.3944628E-02 2.044574 at 20iterations 1.3487365E-03 0.2062550 at 30iterations 1.3165605E-04 2.1031857E-02 at 40iterations 1.2850969E-05 1.9073486E-03 at 50iterations finished qdiffx linear iterations at : 11:51:42 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 1.2850969E-05 1.9073486E-03 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 11:51:42 4.037u 0.268s 0:04.62 92.8% 0+0k 0+0io 6pf+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 Sat Oct 8 2011 at 11:51:42 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 = 2492 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: 1.910110 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): -24.59100 31.32200 ymin,ymax (A): -6.031000 40.33500 zmin,zma (A): 8.618000 50.86600 x,y,z range (A): 55.91300 46.36600 42.24800 scale (grids/A): 1.910110 object centre (A): 3.365500 17.15200 29.74200 number of atom coordinates read : 2492 total number of charged atoms : 2352 net assigned charge : -1.999994 assigned positive charge : 378.3742 centred at (gu) : 89.71291 89.10576 92.64073 assigned negative charge : -380.3746 centred at (gu) : 90.06168 88.70197 92.66653 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 72767 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21567 grid for indexing accessible points = 1.400000 m= 24829 mr = 50484 m= 3779 mr = 18021 m= 275 mr = 2262 m= 2 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 2461 time to turn everything in is 0.6500000 number of dielectric boundary points 30785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 164 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 18488 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) : 0.6367034 object centre at (A) : 3.365500 17.15200 29.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3435635E-03 -1.4629127E-02 midg,1,midg; midg,igrid,midg -1.6602756E-02 3.0587062E-03 1,midg,midg; igrid,midg,midg 2.3543069E-02 -4.7764447E-02 gauss-seidel spectral radius is 0.9986327 estimated iterations to convergence 214 setup time was (sec) 0.9500000 now iterating at: 11:51:43 rms-change max change #iterations 4.164446 176.4760 at 10iterations 1.946015 69.31493 at 20iterations 0.9091427 34.56285 at 30iterations 0.4244419 13.72176 at 40iterations 0.1991390 6.205870 at 50iterations 9.3310058E-02 2.835182 at 60iterations 4.3417133E-02 1.378166 at 70iterations 2.0359173E-02 0.6318741 at 80iterations 9.5530227E-03 0.3100204 at 90iterations 4.4534286E-03 0.1494064 at 100iterations 2.0937691E-03 6.8887711E-02 at 110iterations 9.7862154E-04 3.0833345E-02 at 120iterations finished qdiffx linear iterations at : 11:51:52 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 9.7862154E-04 3.0833345E-02 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 11:51:52 9.322u 0.290s 0:09.93 96.7% 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 Sat Oct 8 2011 at 11:51:52 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 = 2492 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.865165 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): -24.59100 31.32200 ymin,ymax (A): -6.031000 40.33500 zmin,zma (A): 8.618000 50.86600 x,y,z range (A): 55.91300 46.36600 42.24800 scale (grids/A): 2.865165 object centre (A): 3.365500 17.15200 29.74200 number of atom coordinates read : 2492 total number of charged atoms : 2352 net assigned charge : -1.999994 assigned positive charge : 378.3742 centred at (gu) : 89.56920 88.65850 93.96126 assigned negative charge : -380.3746 centred at (gu) : 90.09243 88.05288 93.99972 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 168419 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21567 grid for indexing accessible points = 1.400000 m= 81748 mr = 122470 m= 28271 mr = 66524 m= 6654 mr = 22233 m= 1148 mr = 4967 m= 79 mr = 768 m= 2 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 8308 time to turn everything in is 1.610000 number of dielectric boundary points 69324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 18814 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) : 1.910110 object centre at (A) : 3.365500 17.15200 29.74200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3569408E-02 -0.2257616 midg,1,midg; midg,igrid,midg -0.1658860 -3.5434213E-02 1,midg,midg; igrid,midg,midg 0.2864517 -0.7536263 gauss-seidel spectral radius is 0.9992528 estimated iterations to convergence 289 setup time was (sec) 1.950000 now iterating at: 11:51:54 rms-change max change #iterations 9.709101 355.8203 at 10iterations 5.624146 125.4282 at 20iterations 3.238836 72.13662 at 30iterations 1.854434 33.20612 at 40iterations 1.062853 21.60540 at 50iterations 0.6095612 11.83286 at 60iterations 0.3494864 6.450765 at 70iterations 0.1999296 3.733027 at 80iterations 0.1147515 1.977898 at 90iterations 6.5386280E-02 1.223671 at 100iterations 3.7498999E-02 0.7046747 at 110iterations 2.1438085E-02 0.3853350 at 120iterations 1.2267031E-02 0.2161484 at 130iterations 7.0256484E-03 0.1400061 at 140iterations 4.0143011E-03 7.1718216E-02 at 150iterations 2.2975758E-03 4.2560577E-02 at 160iterations 1.3133294E-03 2.2836685E-02 at 170iterations 7.5056491E-04 1.3816833E-02 at 180iterations finished qdiffx linear iterations at : 11:52:08 total time elapsed so far: 15.35000 # loops : 180 mean,max change (kT/e) : 7.5056491E-04 1.3816833E-02 energy calculations done at 15.35000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.53000 DelPhi exited at 11:52:08 15.527u 0.294s 0:16.14 97.9% 0+0k 0+0io 0pf+0w