Mon Oct 10 14:12:20 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 Mon Oct 10 2011 at 14:12:20 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3324 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: 0.5436276 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): -11.43600 41.81700 ymin,ymax (A): -38.48900 26.99700 zmin,zma (A): -15.94100 34.02100 x,y,z range (A): 53.25300 65.48600 49.96200 scale (grids/A): 0.5436276 object centre (A): 15.19050 -5.746001 9.040000 number of atom coordinates read : 3324 total number of charged atoms : 3181 net assigned charge : 0.5000070 assigned positive charge : 495.0587 centred at (gu) : 90.28856 91.62933 90.49792 assigned negative charge : -494.5600 centred at (gu) : 90.30219 91.55669 90.45372 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6372 nv = 96 ne = 84 npr = 67538 no. pairs analyzed = 67538 no. exposed pairs = 4046 no. arc points = 28531 no. surface atoms = 1372 nbur = 1952 mkacc time = 0.1400000 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= 276 mr = 3452 m= 0 mr = 22 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3174 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2895 ## 411 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8401 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4838467E-10 3.5695497E-10 midg,1,midg; midg,igrid,midg -3.1651751E-10 7.6293838E-10 1,midg,midg; igrid,midg,midg 1.0238283E-10 -7.9725802E-11 gauss-seidel spectral radius is 0.9825790 estimated iterations to convergence 62 setup time was (sec) 0.5600000 now iterating at: 14:12:20 rms-change max change #iterations 7.4770868E-02 12.73995 at 10iterations 5.1176171E-03 1.054886 at 20iterations 4.1031523E-04 6.6970825E-02 at 30iterations 5.7120655E-05 9.2000961E-03 at 40iterations 1.1905996E-05 2.0337105E-03 at 50iterations finished qdiffx linear iterations at : 14:12:23 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 1.1905996E-05 2.0337105E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 14:12:23 3.176u 0.147s 0:03.61 91.6% 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 Mon Oct 10 2011 at 14:12:23 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 = 3324 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: 1.630883 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): -11.43600 41.81700 ymin,ymax (A): -38.48900 26.99700 zmin,zma (A): -15.94100 34.02100 x,y,z range (A): 53.25300 65.48600 49.96200 scale (grids/A): 1.630883 object centre (A): 15.19050 -5.746001 9.040000 number of atom coordinates read : 3324 total number of charged atoms : 3181 net assigned charge : 0.5000070 assigned positive charge : 495.0587 centred at (gu) : 90.86484 94.88708 91.49292 assigned negative charge : -494.5600 centred at (gu) : 90.90623 94.66991 91.36068 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70995 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28531 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22721 mr = 49559 m= 2353 mr = 15937 m= 59 mr = 1152 m= 0 mr = 6 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 271 time to turn everything in is 0.4800000 number of dielectric boundary points 29474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 330 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 24317 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) : 0.5436276 object centre at (A) : 15.19050 -5.746001 9.040000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4898071E-03 2.9897045E-03 midg,1,midg; midg,igrid,midg 6.1467369E-03 1.6798820E-02 1,midg,midg; igrid,midg,midg 4.0224204E-03 1.2940427E-03 gauss-seidel spectral radius is 0.9982074 estimated iterations to convergence 188 setup time was (sec) 0.7500000 now iterating at: 14:12:24 rms-change max change #iterations 3.482052 180.3753 at 10iterations 1.458713 52.15147 at 20iterations 0.6118836 21.05669 at 30iterations 0.2571118 8.856526 at 40iterations 0.1080118 3.554066 at 50iterations 4.5294009E-02 1.688659 at 60iterations 1.9047378E-02 0.7073164 at 70iterations 8.0020316E-03 0.2665987 at 80iterations 3.3754522E-03 0.1303177 at 90iterations 1.4192353E-03 4.8435211E-02 at 100iterations 6.0146576E-04 2.1395206E-02 at 110iterations 2.5636662E-04 8.6193085E-03 at 120iterations finished qdiffx linear iterations at : 14:12:30 total time elapsed so far: 6.670000 # loops : 120 mean,max change (kT/e) : 2.5636662E-04 8.6193085E-03 energy calculations done at 6.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.850000 DelPhi exited at 14:12:31 6.849u 0.164s 0:07.58 92.3% 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 Mon Oct 10 2011 at 14:12:31 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 = 3324 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: 2.446324 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): -11.43600 41.81700 ymin,ymax (A): -38.48900 26.99700 zmin,zma (A): -15.94100 34.02100 x,y,z range (A): 53.25300 65.48600 49.96200 scale (grids/A): 2.446324 object centre (A): 15.19050 -5.746001 9.040000 number of atom coordinates read : 3324 total number of charged atoms : 3181 net assigned charge : 0.5000070 assigned positive charge : 495.0587 centred at (gu) : 91.29704 97.33047 92.23919 assigned negative charge : -494.5600 centred at (gu) : 91.35924 97.00479 92.04081 start vw surface at 0.1800000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 164697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28531 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 79151 mr = 120715 m= 22636 mr = 63518 m= 3609 mr = 17080 m= 241 mr = 2380 m= 4 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 832 time to turn everything in is 1.180000 number of dielectric boundary points 66522 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 25420 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) : 1.630883 object centre at (A) : 15.19050 -5.746001 9.040000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1452440 5.9472509E-02 midg,1,midg; midg,igrid,midg 0.1177178 0.4199761 1,midg,midg; igrid,midg,midg 7.2741956E-02 4.3916121E-02 gauss-seidel spectral radius is 0.9991488 estimated iterations to convergence 271 setup time was (sec) 1.460000 now iterating at: 14:12:33 rms-change max change #iterations 9.042467 301.9189 at 10iterations 5.087129 122.0741 at 20iterations 2.862001 62.20854 at 30iterations 1.596782 33.66893 at 40iterations 0.8883607 18.97772 at 50iterations 0.4951517 10.05741 at 60iterations 0.2750157 5.953512 at 70iterations 0.1524542 3.022623 at 80iterations 8.4528729E-02 1.698902 at 90iterations 4.6657573E-02 0.9672737 at 100iterations 2.5882680E-02 0.5114441 at 110iterations 1.4298805E-02 0.2974176 at 120iterations 7.9144528E-03 0.1762714 at 130iterations 4.3804119E-03 8.5927427E-02 at 140iterations 2.4269363E-03 5.4564953E-02 at 150iterations 1.3496648E-03 2.7008295E-02 at 160iterations 7.5284939E-04 1.7507553E-02 at 170iterations 4.2487241E-04 8.2778931E-03 at 180iterations finished qdiffx linear iterations at : 14:12:44 total time elapsed so far: 12.83000 # loops : 180 mean,max change (kT/e) : 4.2487241E-04 8.2778931E-03 energy calculations done at 12.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 14:12:45 13.035u 0.160s 0:13.70 96.2% 0+0k 0+0io 0pf+0w