Mon Oct 10 17:13:19 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 17:13:19 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: HIZ 236 has a net charge of 0.2000 !!! WARNING: HIZ 251 has a net charge of 0.2000 !!! WARNING: HIY 264 has a net charge of 0.2000 !!! WARNING: HIZ 286 has a net charge of 0.2000 !!! WARNING: HIZ 290 has a net charge of 0.2000 !!! WARNING: HIZ 296 has a net charge of 0.2000 !!! WARNING: ASP 334 has a net charge of -2.0000 !!! WARNING: ZN3 336 has a net charge of 1.4000 !!! WARNING: ZN3 338 has a net charge of 1.4000 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: 0.6770249 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): 26.80700 79.39000 ymin,ymax (A): 2.741000 47.85800 zmin,zma (A): -6.855000 35.02000 x,y,z range (A): 52.58300 45.11700 41.87500 scale (grids/A): 0.6770249 object centre (A): 53.09850 25.29950 14.08250 number of atom coordinates read : 1954 total number of charged atoms : 1825 net assigned charge : -2.499987 assigned positive charge : 279.9312 centred at (gu) : 86.95598 89.72565 90.83913 assigned negative charge : -282.4313 centred at (gu) : 87.12074 89.78365 90.75784 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6168 nv = 96 ne = 84 npr = 40214 no. pairs analyzed = 40214 no. exposed pairs = 2689 no. arc points = 19491 no. surface atoms = 900 nbur = 1054 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 357 mr = 3049 m= 0 mr = 24 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.3200000 number of dielectric boundary points 3452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1749 ## 130 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 6943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4576398E-08 7.6706401E-09 midg,1,midg; midg,igrid,midg 1.4449887E-09 -2.2679256E-08 1,midg,midg; igrid,midg,midg 4.6535327E-08 -2.5889227E-08 gauss-seidel spectral radius is 0.9886410 estimated iterations to convergence 77 setup time was (sec) 0.6700000 now iterating at: 17:13:20 rms-change max change #iterations 0.1620532 26.04609 at 10iterations 1.7881829E-02 2.861763 at 20iterations 1.9639179E-03 0.3296802 at 30iterations 2.1980905E-04 3.0717850E-02 at 40iterations 2.4872603E-05 3.9680228E-03 at 50iterations finished qdiffx linear iterations at : 17:13:24 total time elapsed so far: 4.490000 # loops : 50 mean,max change (kT/e) : 2.4872603E-05 3.9680228E-03 energy calculations done at 4.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.690000 DelPhi exited at 17:13:25 4.699u 0.450s 0:05.55 92.6% 0+0k 0+0io 6pf+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 17:13:25 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: HIZ 236 has a net charge of 0.2000 !!! WARNING: HIZ 251 has a net charge of 0.2000 !!! WARNING: HIY 264 has a net charge of 0.2000 !!! WARNING: HIZ 286 has a net charge of 0.2000 !!! WARNING: HIZ 290 has a net charge of 0.2000 !!! WARNING: HIZ 296 has a net charge of 0.2000 !!! WARNING: ASP 334 has a net charge of -2.0000 !!! WARNING: ZN3 336 has a net charge of 1.4000 !!! WARNING: ZN3 338 has a net charge of 1.4000 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: 2.031075 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): 26.80700 79.39000 ymin,ymax (A): 2.741000 47.85800 zmin,zma (A): -6.855000 35.02000 x,y,z range (A): 52.58300 45.11700 41.87500 scale (grids/A): 2.031075 object centre (A): 53.09850 25.29950 14.08250 number of atom coordinates read : 1954 total number of charged atoms : 1825 net assigned charge : -2.499987 assigned positive charge : 279.9312 centred at (gu) : 80.86803 89.17706 92.51756 assigned negative charge : -282.4313 centred at (gu) : 81.36244 89.35104 92.27361 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 65531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19491 grid for indexing accessible points = 1.400000 m= 21956 mr = 42247 m= 3299 mr = 15104 m= 176 mr = 1867 m= 7 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 686 time to turn everything in is 0.6800000 number of dielectric boundary points 31688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 14480 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) : 0.6770249 object centre at (A) : 53.09850 25.29950 14.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2241683E-02 7.5246854E-04 midg,1,midg; midg,igrid,midg 2.6399862E-02 -4.0512685E-02 1,midg,midg; igrid,midg,midg 6.3750453E-02 -4.1659620E-02 gauss-seidel spectral radius is 0.9987457 estimated iterations to convergence 224 setup time was (sec) 1.080000 now iterating at: 17:13:26 rms-change max change #iterations 4.029115 179.5481 at 10iterations 1.940021 92.89375 at 20iterations 0.9399636 31.76819 at 30iterations 0.4525529 15.94615 at 40iterations 0.2179925 7.406537 at 50iterations 0.1053126 3.561609 at 60iterations 5.0992329E-02 1.711715 at 70iterations 2.4603298E-02 0.9429989 at 80iterations 1.1866269E-02 0.3747387 at 90iterations 5.6938576E-03 0.1872501 at 100iterations 2.7564846E-03 9.5228195E-02 at 110iterations 1.3277865E-03 4.3441772E-02 at 120iterations finished qdiffx linear iterations at : 17:13:36 total time elapsed so far: 10.89000 # loops : 120 mean,max change (kT/e) : 1.3277865E-03 4.3441772E-02 energy calculations done at 10.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.11000 DelPhi exited at 17:13:37 11.118u 0.457s 0:12.00 96.3% 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 17:13:37 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: 254 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1954 !!! WARNING: HIZ 236 has a net charge of 0.2000 !!! WARNING: HIZ 251 has a net charge of 0.2000 !!! WARNING: HIY 264 has a net charge of 0.2000 !!! WARNING: HIZ 286 has a net charge of 0.2000 !!! WARNING: HIZ 290 has a net charge of 0.2000 !!! WARNING: HIZ 296 has a net charge of 0.2000 !!! WARNING: ASP 334 has a net charge of -2.0000 !!! WARNING: ZN3 336 has a net charge of 1.4000 !!! WARNING: ZN3 338 has a net charge of 1.4000 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: 3.046612 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): 26.80700 79.39000 ymin,ymax (A): 2.741000 47.85800 zmin,zma (A): -6.855000 35.02000 x,y,z range (A): 52.58300 45.11700 41.87500 scale (grids/A): 3.046612 object centre (A): 53.09850 25.29950 14.08250 number of atom coordinates read : 1954 total number of charged atoms : 1825 net assigned charge : -2.499987 assigned positive charge : 279.9312 centred at (gu) : 76.30208 88.76566 93.77631 assigned negative charge : -282.4313 centred at (gu) : 77.04366 89.02659 93.41048 start vw surface at 0.1400000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 151398 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19491 grid for indexing accessible points = 1.400000 m= 71310 mr = 103279 m= 24534 mr = 55888 m= 5661 mr = 18718 m= 759 mr = 4006 m= 69 mr = 498 m= 3 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 2493 time to turn everything in is 1.770000 number of dielectric boundary points 71307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 14600 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) : 2.031075 object centre at (A) : 53.09850 25.29950 14.08250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1254932 -6.8056487E-02 midg,1,midg; midg,igrid,midg 0.2663570 -0.5063117 1,midg,midg; igrid,midg,midg 0.9806447 -0.4201814 gauss-seidel spectral radius is 0.9992983 estimated iterations to convergence 298 setup time was (sec) 2.140000 now iterating at: 17:13:40 rms-change max change #iterations 9.357961 477.2294 at 10iterations 5.545971 156.9316 at 20iterations 3.272628 77.83028 at 30iterations 1.934689 46.24303 at 40iterations 1.138931 25.22176 at 50iterations 0.6680067 13.98132 at 60iterations 0.3923142 7.871736 at 70iterations 0.2288204 4.833765 at 80iterations 0.1339662 2.824170 at 90iterations 7.8213379E-02 1.620989 at 100iterations 4.5670718E-02 0.8631544 at 110iterations 2.6710058E-02 0.5087700 at 120iterations 1.5531722E-02 0.2912445 at 130iterations 9.0718698E-03 0.1698251 at 140iterations 5.2944077E-03 0.1056423 at 150iterations 3.0880438E-03 5.5825710E-02 at 160iterations 1.8036178E-03 3.3355713E-02 at 170iterations 1.0515667E-03 2.0721436E-02 at 180iterations finished qdiffx linear iterations at : 17:13:56 total time elapsed so far: 18.46000 # loops : 180 mean,max change (kT/e) : 1.0515667E-03 2.0721436E-02 energy calculations done at 18.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.67000 DelPhi exited at 17:13:57 18.670u 0.496s 0:19.77 96.9% 0+0k 0+0io 0pf+0w