Tue Oct 11 04:19:45 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 04:19:45 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6629793 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): -10.75100 37.45700 ymin,ymax (A): -25.57900 22.67100 zmin,zma (A): -8.642000 45.05500 x,y,z range (A): 48.20800 48.25000 53.69700 scale (grids/A): 0.6629793 object centre (A): 13.35300 -1.454000 18.20650 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 3.154011 assigned positive charge : 416.5338 centred at (gu) : 89.88227 90.24332 91.37079 assigned negative charge : -413.3804 centred at (gu) : 89.60905 90.05357 91.33202 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8005 nv = 96 ne = 84 npr = 56384 no. pairs analyzed = 56384 no. exposed pairs = 3363 no. arc points = 22977 no. surface atoms = 1120 nbur = 1613 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4580 m= 4 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.3500000 number of dielectric boundary points 3831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2245 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9482 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.0963601E-11 2.3134088E-08 midg,1,midg; midg,igrid,midg -3.3514130E-08 5.3528680E-08 1,midg,midg; igrid,midg,midg -5.6621758E-08 6.7232826E-08 gauss-seidel spectral radius is 0.9882151 estimated iterations to convergence 75 setup time was (sec) 0.6400000 now iterating at: 04:19:46 rms-change max change #iterations 0.1744919 27.12000 at 10iterations 1.9396724E-02 2.613693 at 20iterations 2.2056287E-03 0.3111992 at 30iterations 3.1339115E-04 4.0405273E-02 at 40iterations 6.9990696E-05 9.6588135E-03 at 50iterations finished qdiffx linear iterations at : 04:19:50 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 6.9990696E-05 9.6588135E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 04:19:50 4.169u 0.279s 0:04.90 90.4% 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 Tue Oct 11 2011 at 04:19:50 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 1.988938 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): -10.75100 37.45700 ymin,ymax (A): -25.57900 22.67100 zmin,zma (A): -8.642000 45.05500 x,y,z range (A): 48.20800 48.25000 53.69700 scale (grids/A): 1.988938 object centre (A): 13.35300 -1.454000 18.20650 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 3.154011 assigned positive charge : 416.5338 centred at (gu) : 89.64647 90.72948 94.11193 assigned negative charge : -413.3804 centred at (gu) : 88.82693 90.16022 93.99577 start vw surface at 0.1400000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 86242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22977 grid for indexing accessible points = 1.400000 m= 32084 mr = 61355 m= 5228 mr = 23959 m= 358 mr = 3279 m= 6 mr = 128 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 2224 time to turn everything in is 0.7500000 number of dielectric boundary points 35197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 133 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 20408 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) : 0.6629793 object centre at (A) : 13.35300 -1.454000 18.20650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1547005E-02 6.6899559E-03 midg,1,midg; midg,igrid,midg -1.7384814E-02 3.9540008E-02 1,midg,midg; igrid,midg,midg -2.1093596E-02 7.8875892E-02 gauss-seidel spectral radius is 0.9987544 estimated iterations to convergence 224 setup time was (sec) 1.060000 now iterating at: 04:19:52 rms-change max change #iterations 4.782265 211.4757 at 10iterations 2.327607 72.26057 at 20iterations 1.123048 32.73445 at 30iterations 0.5469733 15.68968 at 40iterations 0.2652727 7.388794 at 50iterations 0.1285442 4.073059 at 60iterations 6.2703989E-02 1.893650 at 70iterations 3.0319592E-02 0.8756169 at 80iterations 1.4760724E-02 0.4446566 at 90iterations 7.1715266E-03 0.2009583 at 100iterations 3.4944527E-03 0.1018219 at 110iterations 1.7078283E-03 4.9629211E-02 at 120iterations finished qdiffx linear iterations at : 04:20:00 total time elapsed so far: 9.630000 # loops : 120 mean,max change (kT/e) : 1.7078283E-03 4.9629211E-02 energy calculations done at 9.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.810000 DelPhi exited at 04:20:01 9.816u 0.324s 0:10.73 94.4% 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 Tue Oct 11 2011 at 04:20:01 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: 319 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2733 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 2.983407 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): -10.75100 37.45700 ymin,ymax (A): -25.57900 22.67100 zmin,zma (A): -8.642000 45.05500 x,y,z range (A): 48.20800 48.25000 53.69700 scale (grids/A): 2.983407 object centre (A): 13.35300 -1.454000 18.20650 number of atom coordinates read : 2733 total number of charged atoms : 2581 net assigned charge : 3.154011 assigned positive charge : 416.5338 centred at (gu) : 89.46945 91.09402 96.16788 assigned negative charge : -413.3804 centred at (gu) : 88.24048 90.24014 95.99359 start vw surface at 0.1600000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 199401 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22977 grid for indexing accessible points = 1.400000 m= 103237 mr = 148125 m= 37862 mr = 85394 m= 9340 mr = 30548 m= 1417 mr = 6939 m= 97 mr = 957 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 1.220000 no. cavity mid-points inaccessible to solvent = 7462 time to turn everything in is 2.010000 number of dielectric boundary points 79351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 20636 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) : 1.988938 object centre at (A) : 13.35300 -1.454000 18.20650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4591729 0.2714385 midg,1,midg; midg,igrid,midg -0.1693572 0.4447170 1,midg,midg; igrid,midg,midg -0.1590288 0.6808012 gauss-seidel spectral radius is 0.9992876 estimated iterations to convergence 296 setup time was (sec) 2.330000 now iterating at: 04:20:04 rms-change max change #iterations 11.03884 465.1636 at 10iterations 6.492700 149.8857 at 20iterations 3.812883 74.41154 at 30iterations 2.235686 43.46133 at 40iterations 1.310849 23.30690 at 50iterations 0.7666529 15.76189 at 60iterations 0.4474603 8.858666 at 70iterations 0.2617818 4.095867 at 80iterations 0.1522321 2.725945 at 90iterations 8.8757716E-02 1.733585 at 100iterations 5.1829025E-02 0.9277401 at 110iterations 3.0254479E-02 0.5274382 at 120iterations 1.7636837E-02 0.3232660 at 130iterations 1.0311997E-02 0.1761096 at 140iterations 6.0664681E-03 0.1055744 at 150iterations 3.5994845E-03 7.2759628E-02 at 160iterations 2.1569522E-03 3.9981842E-02 at 170iterations 1.3227635E-03 2.4490356E-02 at 180iterations finished qdiffx linear iterations at : 04:20:18 total time elapsed so far: 16.64000 # loops : 180 mean,max change (kT/e) : 1.3227635E-03 2.4490356E-02 energy calculations done at 16.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.81000 DelPhi exited at 04:20:19 16.817u 0.353s 0:17.50 98.0% 0+0k 0+0io 0pf+0w