Tue Oct 11 06:53:33 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+sph2.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 = amb2.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 Tue Oct 11 2011 at 06:53:33 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3162 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 0.5544913 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): -19.96900 44.23400 ymin,ymax (A): 19.45200 77.34900 zmin,zma (A): -69.40701 -21.49500 x,y,z range (A): 64.20300 57.89700 47.91200 scale (grids/A): 0.5544913 object centre (A): 12.13250 48.40050 -45.45100 number of atom coordinates read : 3162 total number of charged atoms : 3017 net assigned charge : -3.085989 assigned positive charge : 468.2092 centred at (gu) : 89.87258 90.08532 89.97310 assigned negative charge : -471.2959 centred at (gu) : 89.94044 90.28339 90.00841 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6254 nv = 96 ne = 84 npr = 65618 no. pairs analyzed = 65618 no. exposed pairs = 4051 no. arc points = 28450 no. surface atoms = 1367 nbur = 1795 mkacc time = 0.1300000 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 = 1.568000 m= 306 mr = 3238 m= 0 mr = 23 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3600000 number of dielectric boundary points 3299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2852 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8208 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5918029E-11 -6.0201844E-10 midg,1,midg; midg,igrid,midg 1.5671433E-09 -2.2700062E-09 1,midg,midg; igrid,midg,midg 3.9813605E-10 -8.9563740E-10 gauss-seidel spectral radius is 0.9832419 estimated iterations to convergence 64 setup time was (sec) 0.6100000 now iterating at: 06:53:34 rms-change max change #iterations 8.3220497E-02 14.36402 at 10iterations 5.8026826E-03 0.8814492 at 20iterations 4.1764730E-04 6.5607071E-02 at 30iterations 3.9729399E-05 6.9828033E-03 at 40iterations 6.9261209E-06 1.4553070E-03 at 50iterations finished qdiffx linear iterations at : 06:53:37 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 6.9261209E-06 1.4553070E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 06:53:37 3.511u 0.201s 0:04.06 91.3% 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 Tue Oct 11 2011 at 06:53:37 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3162 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 1.663474 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): -19.96900 44.23400 ymin,ymax (A): 19.45200 77.34900 zmin,zma (A): -69.40701 -21.49500 x,y,z range (A): 64.20300 57.89700 47.91200 scale (grids/A): 1.663474 object centre (A): 12.13250 48.40050 -45.45100 number of atom coordinates read : 3162 total number of charged atoms : 3017 net assigned charge : -3.085989 assigned positive charge : 468.2092 centred at (gu) : 89.61737 90.25536 89.91875 assigned negative charge : -471.2959 centred at (gu) : 89.82078 90.84969 90.02473 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68226 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28450 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23021 mr = 45623 m= 3061 mr = 16424 m= 96 mr = 1771 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 493 time to turn everything in is 0.5200000 number of dielectric boundary points 30563 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 279 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 23248 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) : 0.5544913 object centre at (A) : 12.13250 48.40050 -45.45100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4212275E-03 1.0615630E-02 midg,1,midg; midg,igrid,midg 9.8104984E-04 -1.1767639E-02 1,midg,midg; igrid,midg,midg 6.7832759E-03 -3.5648245E-02 gauss-seidel spectral radius is 0.9982758 estimated iterations to convergence 191 setup time was (sec) 0.8200000 now iterating at: 06:53:38 rms-change max change #iterations 3.550734 199.6403 at 10iterations 1.514089 53.55920 at 20iterations 0.6429178 21.91907 at 30iterations 0.2737805 9.107830 at 40iterations 0.1167790 3.867182 at 50iterations 4.9668036E-02 1.696538 at 60iterations 2.1241507E-02 0.7141581 at 70iterations 9.0386700E-03 0.3409762 at 80iterations 3.8623884E-03 0.1353188 at 90iterations 1.6552961E-03 5.4645538E-02 at 100iterations 7.0703815E-04 2.2927284E-02 at 110iterations 3.0341418E-04 1.0513306E-02 at 120iterations finished qdiffx linear iterations at : 06:53:45 total time elapsed so far: 7.490000 # loops : 120 mean,max change (kT/e) : 3.0341418E-04 1.0513306E-02 energy calculations done at 7.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 06:53:46 7.663u 0.250s 0:08.41 94.0% 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 Tue Oct 11 2011 at 06:53:46 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3162 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: UMP 317 has a net charge of -0.1000 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: 2.495211 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): -19.96900 44.23400 ymin,ymax (A): 19.45200 77.34900 zmin,zma (A): -69.40701 -21.49500 x,y,z range (A): 64.20300 57.89700 47.91200 scale (grids/A): 2.495211 object centre (A): 12.13250 48.40050 -45.45100 number of atom coordinates read : 3162 total number of charged atoms : 3017 net assigned charge : -3.085989 assigned positive charge : 468.2092 centred at (gu) : 89.42582 90.38281 89.87777 assigned negative charge : -471.2959 centred at (gu) : 89.73080 91.27430 90.03716 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 157826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28450 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 75809 mr = 111574 m= 25875 mr = 60300 m= 5203 mr = 20440 m= 474 mr = 3751 m= 15 mr = 261 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 1762 time to turn everything in is 1.220000 number of dielectric boundary points 68874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 24112 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) : 1.663474 object centre at (A) : 12.13250 48.40050 -45.45100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1175266 0.2142022 midg,1,midg; midg,igrid,midg -2.6724778E-02 -0.1100816 1,midg,midg; igrid,midg,midg 5.3625375E-02 -0.7954610 gauss-seidel spectral radius is 0.9991705 estimated iterations to convergence 274 setup time was (sec) 1.540000 now iterating at: 06:53:47 rms-change max change #iterations 9.147768 356.3477 at 10iterations 5.171699 133.4893 at 20iterations 2.911679 64.15713 at 30iterations 1.636550 36.99362 at 40iterations 0.9142457 18.91441 at 50iterations 0.5102689 10.38940 at 60iterations 0.2851021 6.050834 at 70iterations 0.1590439 3.038185 at 80iterations 8.8516921E-02 1.828512 at 90iterations 4.9126647E-02 0.9897556 at 100iterations 2.7347578E-02 0.6104927 at 110iterations 1.5187011E-02 0.3009605 at 120iterations 8.4488001E-03 0.1642380 at 130iterations 4.6916637E-03 9.7396076E-02 at 140iterations 2.6165778E-03 5.5397034E-02 at 150iterations 1.4569396E-03 2.9563904E-02 at 160iterations 8.1329630E-04 1.5548706E-02 at 170iterations 4.5873536E-04 8.5535049E-03 at 180iterations finished qdiffx linear iterations at : 06:53:58 total time elapsed so far: 12.39000 # loops : 180 mean,max change (kT/e) : 4.5873536E-04 8.5535049E-03 energy calculations done at 12.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 06:53:59 12.570u 0.261s 0:13.69 93.7% 0+0k 0+0io 0pf+0w