Sat Oct 8 16:49:01 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 16:49:01 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 = 3578 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5577927 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): 15.51200 79.33500 ymin,ymax (A): 128.7920 184.7850 zmin,zma (A): -1.406000 60.42700 x,y,z range (A): 63.82300 55.99298 61.83300 scale (grids/A): 0.5577927 object centre (A): 47.42350 156.7885 29.51050 number of atom coordinates read : 3578 total number of charged atoms : 3427 net assigned charge : -2.499979 assigned positive charge : 538.4718 centred at (gu) : 91.50299 89.36300 88.20183 assigned negative charge : -540.9728 centred at (gu) : 91.44881 89.20201 88.24937 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7345 nv = 96 ne = 84 npr = 70664 no. pairs analyzed = 70664 no. exposed pairs = 4732 no. arc points = 32517 no. surface atoms = 1584 nbur = 1994 mkacc time = 0.1600000 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 = 1.540000 m= 355 mr = 3804 m= 0 mr = 17 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3879 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3258 ## 387 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9533 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3270133E-10 -5.4573129E-10 midg,1,midg; midg,igrid,midg -2.6710996E-09 1.4548126E-09 1,midg,midg; igrid,midg,midg -6.4325839E-10 6.1132571E-10 gauss-seidel spectral radius is 0.9834740 estimated iterations to convergence 64 setup time was (sec) 0.6000000 now iterating at: 16:49:01 rms-change max change #iterations 9.0874851E-02 16.00656 at 10iterations 6.4708339E-03 1.088608 at 20iterations 5.3486926E-04 9.5219612E-02 at 30iterations 1.3653137E-04 1.9047260E-02 at 40iterations 6.4622640E-05 9.3245506E-03 at 50iterations finished qdiffx linear iterations at : 16:49:04 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 6.4622640E-05 9.3245506E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 16:49:05 3.466u 0.208s 0:03.96 92.4% 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 16:49:05 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3578 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: 1.673378 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): 15.51200 79.33500 ymin,ymax (A): 128.7920 184.7850 zmin,zma (A): -1.406000 60.42700 x,y,z range (A): 63.82300 55.99298 61.83300 scale (grids/A): 1.673378 object centre (A): 47.42350 156.7885 29.51050 number of atom coordinates read : 3578 total number of charged atoms : 3427 net assigned charge : -2.499979 assigned positive charge : 538.4718 centred at (gu) : 94.50832 88.08811 84.60485 assigned negative charge : -540.9728 centred at (gu) : 94.34584 87.60540 84.74781 start vw surface at 0.1800000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 81555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32517 grid for indexing accessible points = 1.400000 m= 25873 mr = 55380 m= 3117 mr = 17506 m= 98 mr = 1620 m= 0 mr = 16 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 36121 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 340 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 26466 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) : 0.5577927 object centre at (A) : 47.42350 156.7885 29.51050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.9388881E-03 9.7643184E-03 midg,1,midg; midg,igrid,midg -2.0278543E-02 1.8403230E-02 1,midg,midg; igrid,midg,midg -2.0562762E-02 -1.8237993E-02 gauss-seidel spectral radius is 0.9983490 estimated iterations to convergence 195 setup time was (sec) 0.8200000 now iterating at: 16:49:06 rms-change max change #iterations 3.907050 159.9667 at 10iterations 1.696113 53.47173 at 20iterations 0.7372609 24.55137 at 30iterations 0.3208211 10.74094 at 40iterations 0.1389876 4.098594 at 50iterations 6.0440674E-02 2.165131 at 60iterations 2.6306417E-02 0.8473899 at 70iterations 1.1485421E-02 0.4206142 at 80iterations 5.0050342E-03 0.1527481 at 90iterations 2.2002955E-03 6.8428040E-02 at 100iterations 9.8320108E-04 3.1380653E-02 at 110iterations 4.5996797E-04 1.4998436E-02 at 120iterations finished qdiffx linear iterations at : 16:49:12 total time elapsed so far: 6.830000 # loops : 120 mean,max change (kT/e) : 4.5996797E-04 1.4998436E-02 energy calculations done at 6.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.000000 DelPhi exited at 16:49:12 6.999u 0.177s 0:07.46 95.9% 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 16:49:12 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 = 3578 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.510067 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): 15.51200 79.33500 ymin,ymax (A): 128.7920 184.7850 zmin,zma (A): -1.406000 60.42700 x,y,z range (A): 63.82300 55.99298 61.83300 scale (grids/A): 2.510067 object centre (A): 47.42350 156.7885 29.51050 number of atom coordinates read : 3578 total number of charged atoms : 3427 net assigned charge : -2.499979 assigned positive charge : 538.4718 centred at (gu) : 96.76216 87.13200 81.90721 assigned negative charge : -540.9728 centred at (gu) : 96.51883 86.40813 82.12164 start vw surface at 0.1700000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 189355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32517 grid for indexing accessible points = 1.400000 m= 88477 mr = 135685 m= 26466 mr = 69287 m= 5055 mr = 19624 m= 436 mr = 3457 m= 16 mr = 222 m= 0 mr = 3 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.350000 number of dielectric boundary points 81527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 27393 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) : 1.673378 object centre at (A) : 47.42350 156.7885 29.51050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2087776 0.2606346 midg,1,midg; midg,igrid,midg -0.2837728 0.2916292 1,midg,midg; igrid,midg,midg -0.3724667 -0.3240499 gauss-seidel spectral radius is 0.9992102 estimated iterations to convergence 281 setup time was (sec) 1.640000 now iterating at: 16:49:14 rms-change max change #iterations 10.11014 306.0295 at 10iterations 5.901810 168.3884 at 20iterations 3.421368 88.06275 at 30iterations 1.969597 43.63353 at 40iterations 1.128349 24.62339 at 50iterations 0.6446142 12.15541 at 60iterations 0.3672950 6.704977 at 70iterations 0.2084681 4.246590 at 80iterations 0.1182397 2.086704 at 90iterations 6.7046888E-02 1.318321 at 100iterations 3.7942216E-02 0.7531548 at 110iterations 2.1489436E-02 0.4015312 at 120iterations 1.2148759E-02 0.2425909 at 130iterations 6.8765110E-03 0.1327133 at 140iterations 3.8792961E-03 7.1762085E-02 at 150iterations 2.1933957E-03 4.2986155E-02 at 160iterations 1.2417918E-03 2.2429228E-02 at 170iterations 7.0188876E-04 1.2968063E-02 at 180iterations finished qdiffx linear iterations at : 16:49:24 total time elapsed so far: 11.53000 # loops : 180 mean,max change (kT/e) : 7.0188876E-04 1.2968063E-02 energy calculations done at 11.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.70000 DelPhi exited at 16:49:24 11.701u 0.158s 0:12.15 97.5% 0+0k 0+0io 0pf+0w