Tue Oct 11 06:22:59 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 Tue Oct 11 2011 at 06:22:59 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7197154 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): 2.538000 47.21800 ymin,ymax (A): 0.6669999 42.33800 zmin,zma (A): -2.582000 46.88200 x,y,z range (A): 44.68000 41.67100 49.46400 scale (grids/A): 0.7197154 object centre (A): 24.87800 21.50250 22.15000 number of atom coordinates read : 2049 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 90.16721 89.92111 90.33777 assigned negative charge : -304.4261 centred at (gu) : 90.35656 89.89899 90.36584 start vw surface at 0.1400000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7256 nv = 96 ne = 84 npr = 41153 no. pairs analyzed = 41153 no. exposed pairs = 2473 no. arc points = 16772 no. surface atoms = 841 nbur = 1208 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 472 mr = 4208 m= 2 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3445 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1575 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 7926 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0064702E-08 6.4285373E-08 midg,1,midg; midg,igrid,midg 6.5169054E-08 9.0834661E-08 1,midg,midg; igrid,midg,midg 1.8947884E-07 -4.5254438E-08 gauss-seidel spectral radius is 0.9899301 estimated iterations to convergence 81 setup time was (sec) 0.6300000 now iterating at: 06:23:00 rms-change max change #iterations 0.2153620 31.10494 at 10iterations 2.8290641E-02 3.954598 at 20iterations 3.9778412E-03 0.4729614 at 30iterations 6.9898379E-04 9.3711853E-02 at 40iterations 1.7369956E-04 2.2920609E-02 at 50iterations finished qdiffx linear iterations at : 06:23:03 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 1.7369956E-04 2.2920609E-02 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.340000 DelPhi exited at 06:23:04 4.346u 0.402s 0:05.22 90.8% 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 Tue Oct 11 2011 at 06:23:04 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.159146 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): 2.538000 47.21800 ymin,ymax (A): 0.6669999 42.33800 zmin,zma (A): -2.582000 46.88200 x,y,z range (A): 44.68000 41.67100 49.46400 scale (grids/A): 2.159146 object centre (A): 24.87800 21.50250 22.15000 number of atom coordinates read : 2049 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 90.50162 89.76326 91.01324 assigned negative charge : -304.4261 centred at (gu) : 91.06977 89.69705 91.09750 start vw surface at 0.1300000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 76858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16772 grid for indexing accessible points = 1.400000 m= 30960 mr = 55033 m= 6129 mr = 23608 m= 587 mr = 4104 m= 16 mr = 294 m= 0 mr = 2 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8000000 number of dielectric boundary points 31509 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 64 iepsmp to db, and charging done at 0.9300000 number of grid points assigned charge 15281 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) : 0.7197154 object centre at (A) : 24.87800 21.50250 22.15000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8940608E-02 6.9451660E-02 midg,1,midg; midg,igrid,midg 3.7814579E-03 2.8110070E-02 1,midg,midg; igrid,midg,midg 4.6689309E-02 9.7249057E-03 gauss-seidel spectral radius is 0.9988620 estimated iterations to convergence 235 setup time was (sec) 1.140000 now iterating at: 06:23:06 rms-change max change #iterations 4.671468 182.3541 at 10iterations 2.333813 80.55303 at 20iterations 1.177100 35.51062 at 30iterations 0.5866072 18.95986 at 40iterations 0.2958025 9.456242 at 50iterations 0.1482612 4.417597 at 60iterations 7.4363962E-02 2.266651 at 70iterations 3.7329957E-02 1.081067 at 80iterations 1.8825814E-02 0.5549345 at 90iterations 9.6011478E-03 0.2903767 at 100iterations 4.9226056E-03 0.1523972 at 110iterations 2.5692850E-03 7.5241089E-02 at 120iterations finished qdiffx linear iterations at : 06:23:15 total time elapsed so far: 10.53000 # loops : 120 mean,max change (kT/e) : 2.5692850E-03 7.5241089E-02 energy calculations done at 10.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.98000 DelPhi exited at 06:23:16 10.987u 0.461s 0:11.77 97.1% 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 Tue Oct 11 2011 at 06:23:16 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.238719 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): 2.538000 47.21800 ymin,ymax (A): 0.6669999 42.33800 zmin,zma (A): -2.582000 46.88200 x,y,z range (A): 44.68000 41.67100 49.46400 scale (grids/A): 3.238719 object centre (A): 24.87800 21.50250 22.15000 number of atom coordinates read : 2049 total number of charged atoms : 1923 net assigned charge : 6.931010 assigned positive charge : 311.3571 centred at (gu) : 90.75251 89.64490 91.51994 assigned negative charge : -304.4261 centred at (gu) : 91.60455 89.54563 91.64632 start vw surface at 0.1300000 fill in re-entrant regions at 1.000000 boundary points on vw surface= 176901 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16772 grid for indexing accessible points = 1.400000 m= 96391 mr = 132020 m= 39863 mr = 80571 m= 11821 mr = 32986 m= 2367 mr = 9213 m= 302 mr = 1670 m= 12 mr = 195 m= 0 mr = 7 time to grow re-entrant surface = 1.340000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.480000 number of dielectric boundary points 70995 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.640000 number of grid points assigned charge 15384 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) : 2.159146 object centre at (A) : 24.87800 21.50250 22.15000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4777714 0.6802375 midg,1,midg; midg,igrid,midg -1.7842472E-02 0.2102300 1,midg,midg; igrid,midg,midg 0.3391461 0.1865596 gauss-seidel spectral radius is 0.9993010 estimated iterations to convergence 298 setup time was (sec) 2.840000 now iterating at: 06:23:19 rms-change max change #iterations 10.34214 301.1560 at 10iterations 6.145378 136.1531 at 20iterations 3.642714 84.96913 at 30iterations 2.148861 42.26813 at 40iterations 1.269098 26.53481 at 50iterations 0.7485621 13.99675 at 60iterations 0.4409079 9.121979 at 70iterations 0.2593101 4.554355 at 80iterations 0.1524260 2.539991 at 90iterations 8.9774087E-02 1.585764 at 100iterations 5.3025022E-02 1.108111 at 110iterations 3.1472888E-02 0.6553669 at 120iterations 1.8951641E-02 0.3687744 at 130iterations 1.1604113E-02 0.2247391 at 140iterations 7.3752124E-03 0.1401367 at 150iterations 4.9042422E-03 9.2590332E-02 at 160iterations 3.4705095E-03 6.3243866E-02 at 170iterations 2.5949220E-03 4.5349121E-02 at 180iterations finished qdiffx linear iterations at : 06:23:34 total time elapsed so far: 17.78000 # loops : 180 mean,max change (kT/e) : 2.5949220E-03 4.5349121E-02 energy calculations done at 17.78000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.99000 DelPhi exited at 06:23:35 17.995u 0.511s 0:18.84 98.1% 0+0k 0+0io 0pf+0w