Mon Oct 10 14:09:56 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 14:09:56 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3169 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: 0.5594581 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): 6.020000 61.81200 ymin,ymax (A): -26.19200 29.29100 zmin,zma (A): -36.17100 27.46200 x,y,z range (A): 55.79200 55.48300 63.63300 scale (grids/A): 0.5594581 object centre (A): 33.91600 1.549500 -4.354501 number of atom coordinates read : 3169 total number of charged atoms : 2990 net assigned charge : 3.500028 assigned positive charge : 475.0047 centred at (gu) : 89.47227 90.16552 90.16000 assigned negative charge : -471.5059 centred at (gu) : 89.44227 90.14331 90.05237 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6579 nv = 96 ne = 84 npr = 61540 no. pairs analyzed = 61540 no. exposed pairs = 4445 no. arc points = 31489 no. surface atoms = 1482 nbur = 1687 mkacc time = 0.1700000 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= 299 mr = 3124 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3152 ## 379 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8442 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.5793433E-10 1.6534484E-09 midg,1,midg; midg,igrid,midg 1.0451216E-10 6.4557892E-10 1,midg,midg; igrid,midg,midg 1.7548759E-11 6.2546257E-10 gauss-seidel spectral radius is 0.9835456 estimated iterations to convergence 64 setup time was (sec) 0.6500000 now iterating at: 14:09:57 rms-change max change #iterations 8.3828747E-02 14.12933 at 10iterations 5.8970954E-03 0.9324846 at 20iterations 4.4003970E-04 6.6318512E-02 at 30iterations 4.8346803E-05 7.5988770E-03 at 40iterations 1.2257546E-05 1.7509460E-03 at 50iterations finished qdiffx linear iterations at : 14:10:01 total time elapsed so far: 4.430000 # loops : 50 mean,max change (kT/e) : 1.2257546E-05 1.7509460E-03 energy calculations done at 4.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 14:10:01 4.619u 0.383s 0:05.44 91.7% 0+0k 0+0io 5pf+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 14:10:01 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3169 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: 1.678374 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): 6.020000 61.81200 ymin,ymax (A): -26.19200 29.29100 zmin,zma (A): -36.17100 27.46200 x,y,z range (A): 55.79200 55.48300 63.63300 scale (grids/A): 1.678374 object centre (A): 33.91600 1.549500 -4.354501 number of atom coordinates read : 3169 total number of charged atoms : 2990 net assigned charge : 3.500028 assigned positive charge : 475.0047 centred at (gu) : 88.41591 90.49548 90.47894 assigned negative charge : -471.5059 centred at (gu) : 88.32623 90.42928 90.15674 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72380 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31489 grid for indexing accessible points = 1.400000 m= 22812 mr = 47166 m= 2712 mr = 15139 m= 96 mr = 1227 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6200000 number of dielectric boundary points 34466 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 341 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 23008 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) : 0.5594581 object centre at (A) : 33.91600 1.549500 -4.354501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2083579E-03 2.2368055E-02 midg,1,midg; midg,igrid,midg -5.4535465E-03 -9.4299847E-03 1,midg,midg; igrid,midg,midg 1.3427119E-02 7.2571012E-04 gauss-seidel spectral radius is 0.9983271 estimated iterations to convergence 194 setup time was (sec) 0.9300000 now iterating at: 14:10:03 rms-change max change #iterations 3.697368 176.3185 at 10iterations 1.594332 59.09745 at 20iterations 0.6863078 26.14390 at 30iterations 0.2944683 9.994339 at 40iterations 0.1277238 4.541534 at 50iterations 5.5246193E-02 1.981095 at 60iterations 2.3794215E-02 0.8160233 at 70iterations 1.0278039E-02 0.3707690 at 80iterations 4.4374974E-03 0.1506643 at 90iterations 1.9230879E-03 6.1762094E-02 at 100iterations 8.3032658E-04 2.7967691E-02 at 110iterations 3.6016025E-04 1.2299538E-02 at 120iterations finished qdiffx linear iterations at : 14:10:13 total time elapsed so far: 11.56000 # loops : 120 mean,max change (kT/e) : 3.6016025E-04 1.2299538E-02 energy calculations done at 11.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.71000 DelPhi exited at 14:10:14 11.719u 0.436s 0:12.47 97.3% 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 14:10:14 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3169 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: 2.517561 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): 6.020000 61.81200 ymin,ymax (A): -26.19200 29.29100 zmin,zma (A): -36.17100 27.46200 x,y,z range (A): 55.79200 55.48300 63.63300 scale (grids/A): 2.517561 object centre (A): 33.91600 1.549500 -4.354501 number of atom coordinates read : 3169 total number of charged atoms : 2990 net assigned charge : 3.500028 assigned positive charge : 475.0047 centred at (gu) : 87.62362 90.74284 90.71842 assigned negative charge : -471.5059 centred at (gu) : 87.48930 90.64400 90.23504 start vw surface at 0.1400000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 167826 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31489 grid for indexing accessible points = 1.400000 m= 77193 mr = 116042 m= 23389 mr = 59401 m= 4268 mr = 17116 m= 334 mr = 2613 m= 7 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.490000 number of dielectric boundary points 77740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.630000 number of grid points assigned charge 23901 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) : 1.678374 object centre at (A) : 33.91600 1.549500 -4.354501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.4987970E-02 0.2657823 midg,1,midg; midg,igrid,midg 1.6678533E-02 -0.1854656 1,midg,midg; igrid,midg,midg 0.2788731 3.2519195E-02 gauss-seidel spectral radius is 0.9992044 estimated iterations to convergence 280 setup time was (sec) 1.830000 now iterating at: 14:10:16 rms-change max change #iterations 9.641587 271.1106 at 10iterations 5.653239 149.8669 at 20iterations 3.282933 85.15422 at 30iterations 1.889165 43.47628 at 40iterations 1.086376 28.16862 at 50iterations 0.6195615 16.71171 at 60iterations 0.3540993 9.152311 at 70iterations 0.2013078 4.182714 at 80iterations 0.1141057 2.759329 at 90iterations 6.4794809E-02 1.444962 at 100iterations 3.6682323E-02 0.8035126 at 110iterations 2.0735249E-02 0.4429607 at 120iterations 1.1724070E-02 0.2290063 at 130iterations 6.6255024E-03 0.1348553 at 140iterations 3.7322266E-03 7.2967529E-02 at 150iterations 2.1097478E-03 4.2935371E-02 at 160iterations 1.1954103E-03 2.4127960E-02 at 170iterations 6.7381491E-04 1.3890937E-02 at 180iterations finished qdiffx linear iterations at : 14:10:33 total time elapsed so far: 18.11000 # loops : 180 mean,max change (kT/e) : 6.7381491E-04 1.3890937E-02 energy calculations done at 18.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.27000 DelPhi exited at 14:10:33 18.273u 0.469s 0:19.15 97.8% 0+0k 0+0io 0pf+0w