Sun Oct 9 08:24:25 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 08:24:25 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5829 !!! WARNING: HIR 1428 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 0.5139087 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): -2.652000 66.62100 ymin,ymax (A): -30.47700 36.50200 zmin,zma (A): 26.83800 92.44800 x,y,z range (A): 69.27300 66.97900 65.61000 scale (grids/A): 0.5139087 object centre (A): 31.98450 3.012501 59.64300 number of atom coordinates read : 5829 total number of charged atoms : 5659 net assigned charge : -6.985940 assigned positive charge : 874.6549 centred at (gu) : 90.29511 91.01430 90.31997 assigned negative charge : -881.6476 centred at (gu) : 90.26003 90.99477 90.37678 start vw surface at 0.2400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 9813 nv = 96 ne = 84 npr = 117776 no. pairs analyzed = 117776 no. exposed pairs = 7285 no. arc points = 50360 no. surface atoms = 2447 nbur = 3382 mkacc time = 0.2500000 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 = 1.680000 m= 359 mr = 5064 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.5400000 number of dielectric boundary points 5098 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4992 ## 705 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 13150 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4520307E-11 -3.5465034E-10 midg,1,midg; midg,igrid,midg -1.4430987E-10 -5.5241679E-11 1,midg,midg; igrid,midg,midg -2.2693993E-10 1.4904437E-11 gauss-seidel spectral radius is 0.9807127 estimated iterations to convergence 59 setup time was (sec) 0.7600000 now iterating at: 08:24:26 rms-change max change #iterations 7.9732917E-02 12.29880 at 10iterations 4.9145534E-03 0.7508316 at 20iterations 5.6173420E-04 0.1325417 at 30iterations 1.5221925E-04 3.6666870E-02 at 40iterations 4.8339298E-05 1.0852814E-02 at 50iterations finished qdiffx linear iterations at : 08:24:29 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 4.8339298E-05 1.0852814E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 08:24:29 3.531u 0.201s 0:04.00 93.2% 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 08:24:29 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5829 !!! WARNING: HIR 1428 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= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.541726 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): -2.652000 66.62100 ymin,ymax (A): -30.47700 36.50200 zmin,zma (A): 26.83800 92.44800 x,y,z range (A): 69.27300 66.97900 65.61000 scale (grids/A): 1.541726 object centre (A): 31.98450 3.012501 59.64300 number of atom coordinates read : 5829 total number of charged atoms : 5659 net assigned charge : -6.985940 assigned positive charge : 874.6549 centred at (gu) : 90.88363 93.04121 90.95845 assigned negative charge : -881.6476 centred at (gu) : 90.78002 92.98426 91.12964 start vw surface at 0.2200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 110494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50360 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 32528 mr = 75902 m= 2824 mr = 21506 m= 57 mr = 1205 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1790 time to turn everything in is 0.7600000 number of dielectric boundary points 47290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 637 ## 10 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 42564 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) : 0.5139087 object centre at (A) : 31.98450 3.012501 59.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3011191E-03 -1.3155737E-02 midg,1,midg; midg,igrid,midg -2.0986715E-02 -6.8853889E-03 1,midg,midg; igrid,midg,midg -7.0786499E-03 -7.2277728E-03 gauss-seidel spectral radius is 0.9982387 estimated iterations to convergence 189 setup time was (sec) 1.060000 now iterating at: 08:24:31 rms-change max change #iterations 4.342471 177.9849 at 10iterations 1.838862 52.46216 at 20iterations 0.7755608 23.14940 at 30iterations 0.3296029 9.303427 at 40iterations 0.1391479 3.804938 at 50iterations 5.8930378E-02 1.708920 at 60iterations 2.4981460E-02 0.7377701 at 70iterations 1.0643014E-02 0.3272748 at 80iterations 4.5260214E-03 0.1303635 at 90iterations 1.9554172E-03 5.8254242E-02 at 100iterations 8.4934972E-04 2.6657104E-02 at 110iterations 3.8293569E-04 1.3614655E-02 at 120iterations finished qdiffx linear iterations at : 08:24:37 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 3.8293569E-04 1.3614655E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 08:24:38 7.943u 0.214s 0:08.51 95.7% 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 08:24:38 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5829 !!! WARNING: HIR 1428 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= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.312589 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): -2.652000 66.62100 ymin,ymax (A): -30.47700 36.50200 zmin,zma (A): 26.83800 92.44800 x,y,z range (A): 69.27300 66.97900 65.61000 scale (grids/A): 2.312589 object centre (A): 31.98450 3.012501 59.64300 number of atom coordinates read : 5829 total number of charged atoms : 5659 net assigned charge : -6.985940 assigned positive charge : 874.6549 centred at (gu) : 91.32494 94.56167 91.43739 assigned negative charge : -881.6476 centred at (gu) : 91.16991 94.47637 91.69453 start vw surface at 0.2200000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 256955 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50360 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 116083 mr = 186250 m= 29495 mr = 90211 m= 4077 mr = 21249 m= 208 mr = 2481 m= 1 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 1.080000 no. cavity mid-points inaccessible to solvent = 5988 time to turn everything in is 1.830000 number of dielectric boundary points 106563 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 75 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 45161 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) : 1.541726 object centre at (A) : 31.98450 3.012501 59.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1288590 -0.2934569 midg,1,midg; midg,igrid,midg -0.4618312 -0.3086815 1,midg,midg; igrid,midg,midg 0.1117182 -8.2222804E-02 gauss-seidel spectral radius is 0.9992314 estimated iterations to convergence 285 setup time was (sec) 2.160000 now iterating at: 08:24:40 rms-change max change #iterations 11.81535 288.9502 at 10iterations 7.012687 150.6724 at 20iterations 4.131089 91.25940 at 30iterations 2.422253 46.75789 at 40iterations 1.413727 27.96480 at 50iterations 0.8214743 15.12669 at 60iterations 0.4770612 8.743807 at 70iterations 0.2753346 4.728901 at 80iterations 0.1587712 2.794651 at 90iterations 9.1472983E-02 1.754672 at 100iterations 5.2634265E-02 0.8782806 at 110iterations 3.0226462E-02 0.5153828 at 120iterations 1.7347107E-02 0.2772760 at 130iterations 9.9666519E-03 0.1992455 at 140iterations 5.7228077E-03 9.5754623E-02 at 150iterations 3.2839086E-03 5.6613922E-02 at 160iterations 1.8907993E-03 3.1764984E-02 at 170iterations 1.0929581E-03 1.8835068E-02 at 180iterations finished qdiffx linear iterations at : 08:24:51 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 1.0929581E-03 1.8835068E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.20000 DelPhi exited at 08:24:52 13.197u 0.239s 0:13.79 97.3% 0+0k 0+0io 0pf+0w