Wed Dec 28 11:01:18 PST 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 Wed Dec 28 2011 at 11:01:18 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5749540 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): -41.04500 3.670000 ymin,ymax (A): 13.18400 55.92400 zmin,zma (A): -3.675000 58.24300 x,y,z range (A): 44.71500 42.74000 61.91800 scale (grids/A): 0.5749540 object centre (A): -18.68750 34.55400 27.28400 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 4.000003 assigned positive charge : 285.0061 centred at (gu) : 89.51812 89.56456 89.99930 assigned negative charge : -281.0063 centred at (gu) : 89.59869 89.43272 89.99921 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 4229 nv = 96 ne = 84 npr = 39339 no. pairs analyzed = 39339 no. exposed pairs = 2474 no. arc points = 17189 no. surface atoms = 845 nbur = 1089 mkacc time = 0.1200000 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 = 1.512000 m= 185 mr = 2233 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 2171 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1731 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 5292 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3543177E-10 7.3732442E-10 midg,1,midg; midg,igrid,midg -9.3603481E-10 2.0417290E-09 1,midg,midg; igrid,midg,midg 1.8763098E-09 -1.9255911E-10 gauss-seidel spectral radius is 0.9843016 estimated iterations to convergence 66 setup time was (sec) 0.5500000 now iterating at: 11:01:19 rms-change max change #iterations 7.2787128E-02 14.21934 at 10iterations 5.7148291E-03 1.192660 at 20iterations 4.1733784E-04 9.0702534E-02 at 30iterations 3.2844073E-05 5.6881905E-03 at 40iterations 2.4957474E-06 4.3106079E-04 at 50iterations finished qdiffx linear iterations at : 11:01:23 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 2.4957474E-06 4.3106079E-04 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 11:01:24 4.019u 0.261s 0:05.34 79.9% 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 Wed Dec 28 2011 at 11:01:24 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.724862 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): -41.04500 3.670000 ymin,ymax (A): 13.18400 55.92400 zmin,zma (A): -3.675000 58.24300 x,y,z range (A): 44.71500 42.74000 61.91800 scale (grids/A): 1.724862 object centre (A): -18.68750 34.55400 27.28400 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 4.000003 assigned positive charge : 285.0061 centred at (gu) : 88.55442 88.69379 89.99780 assigned negative charge : -281.0063 centred at (gu) : 88.79628 88.29839 89.99787 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 46170 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17189 grid for indexing accessible points = 1.400000 m= 15144 mr = 31249 m= 1774 mr = 10987 m= 58 mr = 993 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 885 time to turn everything in is 0.4500000 number of dielectric boundary points 19913 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 185 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 13989 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) : 0.5749540 object centre at (A) : -18.68750 34.55400 27.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1490699E-02 1.8592702E-02 midg,1,midg; midg,igrid,midg -4.5687235E-03 3.6267801E-03 1,midg,midg; igrid,midg,midg 1.9115847E-04 7.3906902E-04 gauss-seidel spectral radius is 0.9982538 estimated iterations to convergence 190 setup time was (sec) 0.8000000 now iterating at: 11:01:25 rms-change max change #iterations 2.881339 156.4011 at 10iterations 1.227059 63.08463 at 20iterations 0.5185195 21.80282 at 30iterations 0.2199877 9.958145 at 40iterations 9.3458951E-02 3.756239 at 50iterations 3.9760694E-02 1.542774 at 60iterations 1.6758950E-02 0.6701622 at 70iterations 7.0847245E-03 0.2785745 at 80iterations 3.0087084E-03 0.1178646 at 90iterations 1.2816892E-03 5.2723885E-02 at 100iterations 5.3930067E-04 2.1826744E-02 at 110iterations 2.2919745E-04 8.9874268E-03 at 120iterations finished qdiffx linear iterations at : 11:01:36 total time elapsed so far: 11.20000 # loops : 120 mean,max change (kT/e) : 2.2919745E-04 8.9874268E-03 energy calculations done at 11.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.39000 DelPhi exited at 11:01:37 11.393u 0.476s 0:13.00 91.2% 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 Wed Dec 28 2011 at 11:01:37 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1934 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.587293 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): -41.04500 3.670000 ymin,ymax (A): 13.18400 55.92400 zmin,zma (A): -3.675000 58.24300 x,y,z range (A): 44.71500 42.74000 61.91800 scale (grids/A): 2.587293 object centre (A): -18.68750 34.55400 27.28400 number of atom coordinates read : 1934 total number of charged atoms : 1802 net assigned charge : 4.000003 assigned positive charge : 285.0061 centred at (gu) : 87.83148 88.04068 89.99674 assigned negative charge : -281.0063 centred at (gu) : 88.19460 87.44769 89.99678 start vw surface at 0.1500000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 106886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17189 grid for indexing accessible points = 1.400000 m= 51140 mr = 75823 m= 15855 mr = 41429 m= 2964 mr = 12612 m= 262 mr = 2094 m= 6 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 2965 time to turn everything in is 1.100000 number of dielectric boundary points 45041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 14414 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) : 1.724862 object centre at (A) : -18.68750 34.55400 27.28400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1891378 0.1619358 midg,1,midg; midg,igrid,midg -6.6973992E-02 2.3314180E-02 1,midg,midg; igrid,midg,midg -3.1483468E-02 -4.1924548E-04 gauss-seidel spectral radius is 0.9991270 estimated iterations to convergence 267 setup time was (sec) 1.490000 now iterating at: 11:01:39 rms-change max change #iterations 7.181799 278.0615 at 10iterations 3.992507 143.7170 at 20iterations 2.198379 66.76391 at 30iterations 1.209652 33.08404 at 40iterations 0.6627471 17.47751 at 50iterations 0.3638811 8.273575 at 60iterations 0.1992851 5.632921 at 70iterations 0.1086751 2.748421 at 80iterations 5.9451301E-02 1.412575 at 90iterations 3.2468688E-02 0.7677393 at 100iterations 1.7721329E-02 0.3911705 at 110iterations 9.6693151E-03 0.2507744 at 120iterations 5.2891565E-03 0.1220818 at 130iterations 2.8906930E-03 6.8386078E-02 at 140iterations 1.5796418E-03 3.6602020E-02 at 150iterations 8.6523982E-04 1.8871307E-02 at 160iterations 4.7106988E-04 1.2046576E-02 at 170iterations 2.5731913E-04 5.9814453E-03 at 180iterations finished qdiffx linear iterations at : 11:01:56 total time elapsed so far: 18.46000 # loops : 180 mean,max change (kT/e) : 2.5731913E-04 5.9814453E-03 energy calculations done at 18.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.66000 DelPhi exited at 11:01:56 18.661u 0.476s 0:19.51 98.0% 0+0k 0+0io 0pf+0w