Tue Oct 11 06:22:23 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 Tue Oct 11 2011 at 06:22:23 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 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 : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 90.17486 89.92022 90.33140 assigned negative charge : -304.2972 centred at (gu) : 90.35748 89.89860 90.36646 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 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 = 0.1500000 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 = 0.1800000 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= 1576 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7943 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0028507E-07 6.6283100E-08 midg,1,midg; midg,igrid,midg 7.1994968E-08 9.6808847E-08 1,midg,midg; igrid,midg,midg 1.9138781E-07 -3.4108030E-08 gauss-seidel spectral radius is 0.9899301 estimated iterations to convergence 81 setup time was (sec) 0.6700000 now iterating at: 06:22:24 rms-change max change #iterations 0.2137138 31.10494 at 10iterations 2.7691202E-02 4.087992 at 20iterations 3.7713174E-03 0.4749641 at 30iterations 6.1181904E-04 7.7936172E-02 at 40iterations 1.4102180E-04 1.9441605E-02 at 50iterations finished qdiffx linear iterations at : 06:22:27 total time elapsed so far: 4.190000 # loops : 50 mean,max change (kT/e) : 1.4102180E-04 1.9441605E-02 energy calculations done at 4.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.420000 DelPhi exited at 06:22:28 4.423u 0.445s 0:05.37 90.5% 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 Tue Oct 11 2011 at 06:22:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 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 : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 90.52451 89.76053 90.99409 assigned negative charge : -304.2972 centred at (gu) : 91.07256 89.69588 91.09937 start vw surface at 0.1400000 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 = 0.4300000 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 0.9200000 number of grid points assigned charge 15329 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 6.4264320E-02 7.0246242E-02 midg,1,midg; midg,igrid,midg 4.7757123E-03 2.9514523E-02 1,midg,midg; igrid,midg,midg 4.7737222E-02 1.3948929E-02 gauss-seidel spectral radius is 0.9988620 estimated iterations to convergence 235 setup time was (sec) 1.120000 now iterating at: 06:22:30 rms-change max change #iterations 4.658456 182.3541 at 10iterations 2.327430 80.55309 at 20iterations 1.173814 35.42443 at 30iterations 0.5849374 18.77837 at 40iterations 0.2947359 9.520965 at 50iterations 0.1475874 4.400963 at 60iterations 7.4023321E-02 2.218334 at 70iterations 3.7097946E-02 1.077525 at 80iterations 1.8634548E-02 0.5524092 at 90iterations 9.4358493E-03 0.2841940 at 100iterations 4.7972458E-03 0.1483650 at 110iterations 2.4658307E-03 7.1193695E-02 at 120iterations finished qdiffx linear iterations at : 06:22:39 total time elapsed so far: 10.12000 # loops : 120 mean,max change (kT/e) : 2.4658307E-03 7.1193695E-02 energy calculations done at 10.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.35000 DelPhi exited at 06:22:40 10.352u 0.486s 0:11.22 96.5% 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 06:22:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2049 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 : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 90.78686 89.64082 91.49120 assigned negative charge : -304.2972 centred at (gu) : 91.60875 89.54390 91.64911 start vw surface at 0.1400000 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 2.490000 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 15432 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 0.5247326 0.6859806 midg,1,midg; midg,igrid,midg -8.3593167E-03 0.2208186 1,midg,midg; igrid,midg,midg 0.3472350 0.2226222 gauss-seidel spectral radius is 0.9993010 estimated iterations to convergence 298 setup time was (sec) 2.840000 now iterating at: 06:22:43 rms-change max change #iterations 10.32296 301.1562 at 10iterations 6.134852 136.1612 at 20iterations 3.637012 84.99490 at 30iterations 2.144919 42.26566 at 40iterations 1.266967 25.99943 at 50iterations 0.7472308 13.96954 at 60iterations 0.4400400 9.122513 at 70iterations 0.2587189 4.567301 at 80iterations 0.1519902 2.539978 at 90iterations 8.9416623E-02 1.541389 at 100iterations 5.2672915E-02 1.096561 at 110iterations 3.1119823E-02 0.6588774 at 120iterations 1.8570285E-02 0.3624458 at 130iterations 1.1181992E-02 0.2258797 at 140iterations 6.9280011E-03 0.1282578 at 150iterations 4.4453889E-03 8.1750870E-02 at 160iterations 3.0243360E-03 5.2271843E-02 at 170iterations 2.1831745E-03 3.8471222E-02 at 180iterations finished qdiffx linear iterations at : 06:22:58 total time elapsed so far: 17.78000 # loops : 180 mean,max change (kT/e) : 2.1831745E-03 3.8471222E-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 06:22:58 17.998u 0.556s 0:18.90 98.0% 0+0k 0+0io 0pf+0w