Tue Oct 11 03:22:24 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 Tue Oct 11 2011 at 03:22:24 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3395 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: 0.5482067 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): -34.44700 22.18500 ymin,ymax (A): -4.805000 60.13400 zmin,zma (A): -7.579000 47.37300 x,y,z range (A): 56.63200 64.93900 54.95200 scale (grids/A): 0.5482067 object centre (A): -6.131000 27.66450 19.89700 number of atom coordinates read : 3395 total number of charged atoms : 3234 net assigned charge : 5.000029 assigned positive charge : 505.3322 centred at (gu) : 90.95290 87.64448 88.98122 assigned negative charge : -500.3340 centred at (gu) : 91.08569 87.36732 88.88047 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6920 nv = 96 ne = 84 npr = 64042 no. pairs analyzed = 64042 no. exposed pairs = 5000 no. arc points = 35968 no. surface atoms = 1649 nbur = 1746 mkacc time = 0.1100000 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= 314 mr = 3108 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 4104 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3551 ## 425 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8805 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.2058569E-10 9.4912000E-10 midg,1,midg; midg,igrid,midg -3.4520742E-09 1.4417821E-09 1,midg,midg; igrid,midg,midg 1.1616360E-09 -8.4869356E-10 gauss-seidel spectral radius is 0.9828966 estimated iterations to convergence 63 setup time was (sec) 0.4200000 now iterating at: 03:22:25 rms-change max change #iterations 7.6660834E-02 12.07139 at 10iterations 5.2114073E-03 0.7695370 at 20iterations 4.3071847E-04 7.1949005E-02 at 30iterations 6.1291918E-05 1.0404587E-02 at 40iterations 1.2499811E-05 1.7986298E-03 at 50iterations finished qdiffx linear iterations at : 03:22:28 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.2499811E-05 1.7986298E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 03:22:28 3.464u 0.175s 0:03.97 91.4% 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 03:22:28 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3395 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: 1.644620 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): -34.44700 22.18500 ymin,ymax (A): -4.805000 60.13400 zmin,zma (A): -7.579000 47.37300 x,y,z range (A): 56.63200 64.93900 54.95200 scale (grids/A): 1.644620 object centre (A): -6.131000 27.66450 19.89700 number of atom coordinates read : 3395 total number of charged atoms : 3234 net assigned charge : 5.000029 assigned positive charge : 505.3322 centred at (gu) : 92.85767 82.93233 86.94312 assigned negative charge : -500.3340 centred at (gu) : 93.25653 82.10204 86.64106 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 74598 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35968 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24306 mr = 46644 m= 3126 mr = 15829 m= 108 mr = 1504 m= 0 mr = 9 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 38152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 374 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 24816 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) : 0.5482067 object centre at (A) : -6.131000 27.66450 19.89700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7378306E-03 3.0181489E-03 midg,1,midg; midg,igrid,midg 2.3238437E-02 5.6460664E-02 1,midg,midg; igrid,midg,midg -6.5268506E-03 -2.7515653E-03 gauss-seidel spectral radius is 0.9982833 estimated iterations to convergence 192 setup time was (sec) 0.5900000 now iterating at: 03:22:29 rms-change max change #iterations 3.631410 168.3154 at 10iterations 1.538470 55.98234 at 20iterations 0.6541513 24.41583 at 30iterations 0.2779373 9.198560 at 40iterations 0.1180975 4.022617 at 50iterations 5.0552793E-02 1.657506 at 60iterations 2.1549759E-02 0.6842709 at 70iterations 9.1808345E-03 0.3208723 at 80iterations 3.9174138E-03 0.1311951 at 90iterations 1.6892520E-03 5.8378220E-02 at 100iterations 7.2276714E-04 2.6735306E-02 at 110iterations 3.1036255E-04 1.0746002E-02 at 120iterations finished qdiffx linear iterations at : 03:22:36 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 3.1036255E-04 1.0746002E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 03:22:37 7.966u 0.223s 0:08.48 96.4% 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 03:22:37 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3395 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: 2.466930 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): -34.44700 22.18500 ymin,ymax (A): -4.805000 60.13400 zmin,zma (A): -7.579000 47.37300 x,y,z range (A): 56.63200 64.93900 54.95200 scale (grids/A): 2.466930 object centre (A): -6.131000 27.66450 19.89700 number of atom coordinates read : 3395 total number of charged atoms : 3234 net assigned charge : 5.000029 assigned positive charge : 505.3322 centred at (gu) : 94.28605 79.39811 85.41437 assigned negative charge : -500.3340 centred at (gu) : 94.88484 78.15272 84.96146 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 172850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35968 grid for indexing accessible points = 1.400000 m= 79862 mr = 115442 m= 26057 mr = 60310 m= 4921 mr = 18928 m= 357 mr = 3082 m= 4 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9000000 number of dielectric boundary points 86153 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 25832 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) : 1.644620 object centre at (A) : -6.131000 27.66450 19.89700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1149462 3.9390385E-02 midg,1,midg; midg,igrid,midg 0.4972161 0.9827837 1,midg,midg; igrid,midg,midg -0.1331493 2.6951477E-02 gauss-seidel spectral radius is 0.9991952 estimated iterations to convergence 278 setup time was (sec) 1.130000 now iterating at: 03:22:39 rms-change max change #iterations 9.721547 291.3350 at 10iterations 5.702543 154.6056 at 20iterations 3.302974 83.62553 at 30iterations 1.897001 44.31396 at 40iterations 1.084155 23.44630 at 50iterations 0.6157407 13.46653 at 60iterations 0.3500013 7.654016 at 70iterations 0.1976127 4.145391 at 80iterations 0.1113874 2.172837 at 90iterations 6.2835015E-02 1.270355 at 100iterations 3.5403531E-02 0.7326710 at 110iterations 1.9868070E-02 0.4086914 at 120iterations 1.1173777E-02 0.2267761 at 130iterations 6.2846127E-03 0.1367159 at 140iterations 3.5202170E-03 6.9267273E-02 at 150iterations 1.9793303E-03 4.4825077E-02 at 160iterations 1.1108874E-03 2.1818161E-02 at 170iterations 6.2586670E-04 1.2964487E-02 at 180iterations finished qdiffx linear iterations at : 03:22:50 total time elapsed so far: 12.52000 # loops : 180 mean,max change (kT/e) : 6.2586670E-04 1.2964487E-02 energy calculations done at 12.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 03:22:50 12.684u 0.227s 0:13.19 97.8% 0+0k 0+0io 0pf+0w