Sun Oct 9 10:15:16 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 Sun Oct 9 2011 at 10:15:16 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2180 !!! WARNING: HIR 524 has a net charge of 0.5140 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: 0.6655077 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): -1.271000 48.80800 ymin,ymax (A): -27.12600 26.36700 zmin,zma (A): -5.418000 47.40500 x,y,z range (A): 50.07900 53.49300 52.82300 scale (grids/A): 0.6655077 object centre (A): 23.76850 -0.3795004 20.99350 number of atom coordinates read : 2180 total number of charged atoms : 2043 net assigned charge : 1.514015 assigned positive charge : 316.9337 centred at (gu) : 90.23315 92.62126 91.31989 assigned negative charge : -315.4203 centred at (gu) : 90.27930 92.44413 91.30742 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6724 nv = 96 ne = 84 npr = 43353 no. pairs analyzed = 43353 no. exposed pairs = 2940 no. arc points = 20849 no. surface atoms = 985 nbur = 1195 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 404 mr = 3516 m= 6 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.2700000 number of dielectric boundary points 3564 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1880 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7577 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5992170E-10 7.5443385E-09 midg,1,midg; midg,igrid,midg -1.7103169E-08 6.1757639E-08 1,midg,midg; igrid,midg,midg 1.1349695E-08 -5.2855258E-09 gauss-seidel spectral radius is 0.9882700 estimated iterations to convergence 75 setup time was (sec) 0.4900000 now iterating at: 10:15:17 rms-change max change #iterations 0.1582795 22.60726 at 10iterations 1.7142946E-02 2.410690 at 20iterations 1.8203150E-03 0.2622063 at 30iterations 1.9837065E-04 3.2012939E-02 at 40iterations 2.1500433E-05 3.0536652E-03 at 50iterations finished qdiffx linear iterations at : 10:15:19 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 2.1500433E-05 3.0536652E-03 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 10:15:20 3.054u 0.136s 0:03.49 91.1% 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 10:15:20 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2180 !!! WARNING: HIR 524 has a net charge of 0.5140 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: 1.996523 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): -1.271000 48.80800 ymin,ymax (A): -27.12600 26.36700 zmin,zma (A): -5.418000 47.40500 x,y,z range (A): 50.07900 53.49300 52.82300 scale (grids/A): 1.996523 object centre (A): 23.76850 -0.3795004 20.99350 number of atom coordinates read : 2180 total number of charged atoms : 2043 net assigned charge : 1.514015 assigned positive charge : 316.9337 centred at (gu) : 90.69930 97.86388 93.95951 assigned negative charge : -315.4203 centred at (gu) : 90.83817 97.33276 93.92247 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 71335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20849 grid for indexing accessible points = 1.400000 m= 26079 mr = 47565 m= 4745 mr = 19082 m= 368 mr = 3118 m= 6 mr = 147 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 32621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 92 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 16166 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) : 0.6655077 object centre at (A) : 23.76850 -0.3795004 20.99350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7026540E-02 4.9513418E-02 midg,1,midg; midg,igrid,midg -5.0619040E-03 6.5034717E-02 1,midg,midg; igrid,midg,midg -1.9449599E-02 -3.2549556E-02 gauss-seidel spectral radius is 0.9987197 estimated iterations to convergence 221 setup time was (sec) 0.7600000 now iterating at: 10:15:21 rms-change max change #iterations 4.180330 232.3138 at 10iterations 2.005436 79.79372 at 20iterations 0.9657299 35.66378 at 30iterations 0.4635932 15.84356 at 40iterations 0.2229319 7.204432 at 50iterations 0.1073526 3.620660 at 60iterations 5.1554136E-02 1.821519 at 70iterations 2.4779186E-02 0.7593689 at 80iterations 1.1861064E-02 0.3575435 at 90iterations 5.6991628E-03 0.1936035 at 100iterations 2.7311621E-03 8.8150024E-02 at 110iterations 1.3137930E-03 4.3675423E-02 at 120iterations finished qdiffx linear iterations at : 10:15:27 total time elapsed so far: 6.760000 # loops : 120 mean,max change (kT/e) : 1.3137930E-03 4.3675423E-02 energy calculations done at 6.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.930000 DelPhi exited at 10:15:27 6.929u 0.160s 0:07.36 96.1% 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 10:15:27 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2180 !!! WARNING: HIR 524 has a net charge of 0.5140 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: 2.994785 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): -1.271000 48.80800 ymin,ymax (A): -27.12600 26.36700 zmin,zma (A): -5.418000 47.40500 x,y,z range (A): 50.07900 53.49300 52.82300 scale (grids/A): 2.994785 object centre (A): 23.76850 -0.3795004 20.99350 number of atom coordinates read : 2180 total number of charged atoms : 2043 net assigned charge : 1.514015 assigned positive charge : 316.9337 centred at (gu) : 91.04886 101.7957 95.93921 assigned negative charge : -315.4203 centred at (gu) : 91.25726 100.9992 95.88365 start vw surface at 0.1200000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 165061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20849 grid for indexing accessible points = 1.400000 m= 81608 mr = 115821 m= 31806 mr = 65897 m= 8842 mr = 25778 m= 1588 mr = 6729 m= 103 mr = 1146 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 73597 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 16340 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) : 1.996523 object centre at (A) : 23.76850 -0.3795004 20.99350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7185539E-02 0.4979443 midg,1,midg; midg,igrid,midg -7.6333053E-02 0.4659941 1,midg,midg; igrid,midg,midg -0.2653870 -0.3106248 gauss-seidel spectral radius is 0.9992852 estimated iterations to convergence 295 setup time was (sec) 1.530000 now iterating at: 10:15:29 rms-change max change #iterations 9.601089 477.8455 at 10iterations 5.617288 163.3439 at 20iterations 3.281704 64.73263 at 30iterations 1.918647 45.81564 at 40iterations 1.115913 27.21587 at 50iterations 0.6481661 11.54479 at 60iterations 0.3766022 7.639404 at 70iterations 0.2184635 4.092474 at 80iterations 0.1268678 2.312957 at 90iterations 7.3565364E-02 1.311818 at 100iterations 4.2615604E-02 0.7720947 at 110iterations 2.4745772E-02 0.4522877 at 120iterations 1.4390643E-02 0.2446537 at 130iterations 8.3184950E-03 0.1504233 at 140iterations 4.8329583E-03 9.5397949E-02 at 150iterations 2.8006721E-03 5.1334381E-02 at 160iterations 1.6276380E-03 2.8508663E-02 at 170iterations 9.4083004E-04 1.8543720E-02 at 180iterations finished qdiffx linear iterations at : 10:15:38 total time elapsed so far: 10.95000 # loops : 180 mean,max change (kT/e) : 9.4083004E-04 1.8543720E-02 energy calculations done at 10.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.13000 DelPhi exited at 10:15:39 11.130u 0.188s 0:11.58 97.6% 0+0k 0+0io 0pf+0w