Sun Oct 9 21:11:22 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 Sun Oct 9 2011 at 21:11:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3200 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: 0.6084742 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): 45.62200 98.68500 ymin,ymax (A): 2.968000 61.47500 zmin,zma (A): 14.85100 66.82800 x,y,z range (A): 53.06300 58.50700 51.97701 scale (grids/A): 0.6084742 object centre (A): 72.15350 32.22150 40.83950 number of atom coordinates read : 3200 total number of charged atoms : 3140 net assigned charge : 5.500019 assigned positive charge : 499.2436 centred at (gu) : 90.22588 87.61253 90.59972 assigned negative charge : -493.7450 centred at (gu) : 90.13655 87.53487 90.60832 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8130 nv = 96 ne = 84 npr = 59775 no. pairs analyzed = 59775 no. exposed pairs = 4406 no. arc points = 32268 no. surface atoms = 1457 nbur = 1743 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 433 mr = 4061 m= 3 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.2400000 number of dielectric boundary points 4474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3283 ## 338 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 10216 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2500846E-09 3.0463061E-09 midg,1,midg; midg,igrid,midg -2.7404363E-09 4.5999871E-09 1,midg,midg; igrid,midg,midg -2.0787660E-09 8.9096828E-09 gauss-seidel spectral radius is 0.9860858 estimated iterations to convergence 69 setup time was (sec) 0.4300000 now iterating at: 21:11:23 rms-change max change #iterations 0.1264982 17.77723 at 10iterations 1.1080205E-02 1.484908 at 20iterations 9.7520021E-04 0.1416130 at 30iterations 8.7056273E-05 1.4135361E-02 at 40iterations 7.6462320E-06 1.0528564E-03 at 50iterations finished qdiffx linear iterations at : 21:11:26 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 7.6462320E-06 1.0528564E-03 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 21:11:26 3.473u 0.172s 0:03.92 92.8% 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 Sun Oct 9 2011 at 21:11:26 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 = 3200 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: 1.825423 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): 45.62200 98.68500 ymin,ymax (A): 2.968000 61.47500 zmin,zma (A): 14.85100 66.82800 x,y,z range (A): 53.06300 58.50700 51.97701 scale (grids/A): 1.825423 object centre (A): 72.15350 32.22150 40.83950 number of atom coordinates read : 3200 total number of charged atoms : 3140 net assigned charge : 5.500019 assigned positive charge : 499.2436 centred at (gu) : 90.67667 82.83667 91.79804 assigned negative charge : -493.7450 centred at (gu) : 90.40941 82.60439 91.82425 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 87860 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32268 grid for indexing accessible points = 1.400000 m= 29605 mr = 57781 m= 4452 mr = 20364 m= 280 mr = 2487 m= 6 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1720 time to turn everything in is 0.4400000 number of dielectric boundary points 41484 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 270 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 24594 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) : 0.6084742 object centre at (A) : 72.15350 32.22150 40.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1405062E-03 -1.8866964E-03 midg,1,midg; midg,igrid,midg 4.7890902E-02 2.5983788E-02 1,midg,midg; igrid,midg,midg -1.5697831E-02 1.1189003E-02 gauss-seidel spectral radius is 0.9986000 estimated iterations to convergence 212 setup time was (sec) 0.6500000 now iterating at: 21:11:27 rms-change max change #iterations 4.418956 181.8745 at 10iterations 2.043171 62.52403 at 20iterations 0.9418176 29.48258 at 30iterations 0.4360131 13.39551 at 40iterations 0.2015071 5.997680 at 50iterations 9.3430072E-02 2.818298 at 60iterations 4.3167882E-02 1.261093 at 70iterations 2.0004427E-02 0.5865379 at 80iterations 9.2698913E-03 0.2712302 at 90iterations 4.2976313E-03 0.1306152 at 100iterations 1.9882815E-03 5.8989584E-02 at 110iterations 9.2258694E-04 2.9701233E-02 at 120iterations finished qdiffx linear iterations at : 21:11:34 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 9.2258694E-04 2.9701233E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 21:11:35 7.997u 0.187s 0:08.46 96.5% 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 Sun Oct 9 2011 at 21:11:35 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 = 3200 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: 2.738134 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): 45.62200 98.68500 ymin,ymax (A): 2.968000 61.47500 zmin,zma (A): 14.85100 66.82800 x,y,z range (A): 53.06300 58.50700 51.97701 scale (grids/A): 2.738134 object centre (A): 72.15350 32.22150 40.83950 number of atom coordinates read : 3200 total number of charged atoms : 3140 net assigned charge : 5.500019 assigned positive charge : 499.2436 centred at (gu) : 91.01504 79.25468 92.69700 assigned negative charge : -493.7450 centred at (gu) : 90.61386 78.90645 92.73627 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 203321 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32268 grid for indexing accessible points = 1.400000 m= 97254 mr = 141415 m= 33164 mr = 76336 m= 7810 mr = 25296 m= 1047 mr = 5382 m= 72 mr = 633 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.6299999 no. cavity mid-points inaccessible to solvent = 5803 time to turn everything in is 1.080000 number of dielectric boundary points 93576 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 25118 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) : 1.825423 object centre at (A) : 72.15350 32.22150 40.83950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3582370E-02 -0.1472921 midg,1,midg; midg,igrid,midg 0.4776673 0.2952102 1,midg,midg; igrid,midg,midg -0.1992457 0.1196411 gauss-seidel spectral radius is 0.9992754 estimated iterations to convergence 293 setup time was (sec) 1.320000 now iterating at: 21:11:36 rms-change max change #iterations 10.87648 299.7725 at 10iterations 6.532918 158.9873 at 20iterations 3.875346 83.22318 at 30iterations 2.280073 49.40254 at 40iterations 1.337723 30.06242 at 50iterations 0.7851267 15.73794 at 60iterations 0.4590355 8.669952 at 70iterations 0.2670975 5.325855 at 80iterations 0.1555537 2.782707 at 90iterations 9.0276316E-02 1.696579 at 100iterations 5.2448682E-02 0.9552002 at 110iterations 3.0477855E-02 0.6403809 at 120iterations 1.7689457E-02 0.3110971 at 130iterations 1.0233361E-02 0.1862717 at 140iterations 5.9343129E-03 0.1017871 at 150iterations 3.4438570E-03 6.3123703E-02 at 160iterations 1.9945039E-03 3.7134171E-02 at 170iterations 1.1531507E-03 2.0862579E-02 at 180iterations finished qdiffx linear iterations at : 21:11:48 total time elapsed so far: 13.09000 # loops : 180 mean,max change (kT/e) : 1.1531507E-03 2.0862579E-02 energy calculations done at 13.09000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.22000 DelPhi exited at 21:11:49 13.220u 0.211s 0:13.71 97.9% 0+0k 0+0io 0pf+0w