Sat Oct 15 14:59:04 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 Sat Oct 15 2011 at 14:59:04 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2488 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: 0.6327764 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): 5.400000 60.17700 ymin,ymax (A): 7.645999 55.84300 zmin,zma (A): 6.185000 62.44500 x,y,z range (A): 54.77700 48.19700 56.26000 scale (grids/A): 0.6327764 object centre (A): 32.78850 31.74450 34.31500 number of atom coordinates read : 2488 total number of charged atoms : 2354 net assigned charge : 1.000028 assigned positive charge : 367.2930 centred at (gu) : 88.51283 89.47242 90.34349 assigned negative charge : -366.2939 centred at (gu) : 88.42254 89.52437 90.19785 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6792 nv = 96 ne = 84 npr = 49877 no. pairs analyzed = 49877 no. exposed pairs = 3312 no. arc points = 23713 no. surface atoms = 1116 nbur = 1372 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 389 mr = 3503 m= 5 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3100000 number of dielectric boundary points 3639 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2284 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8118 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1185138E-08 1.5258010E-08 midg,1,midg; midg,igrid,midg 6.6199299E-09 -3.0669651E-09 1,midg,midg; igrid,midg,midg -9.7173825E-09 6.7313657E-09 gauss-seidel spectral radius is 0.9870635 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 14:59:05 rms-change max change #iterations 0.1374164 27.02756 at 10iterations 1.3151768E-02 1.952126 at 20iterations 1.3032528E-03 0.1819286 at 30iterations 1.3089416E-04 1.8035889E-02 at 40iterations 1.3617401E-05 2.2087097E-03 at 50iterations finished qdiffx linear iterations at : 14:59:11 total time elapsed so far: 5.110000 # loops : 50 mean,max change (kT/e) : 1.3617401E-05 2.2087097E-03 energy calculations done at 5.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.280000 DelPhi exited at 14:59:11 5.282u 0.464s 0:07.21 79.6% 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 Sat Oct 15 2011 at 14:59:11 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2488 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: 1.898329 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): 5.400000 60.17700 ymin,ymax (A): 7.645999 55.84300 zmin,zma (A): 6.185000 62.44500 x,y,z range (A): 54.77700 48.19700 56.26000 scale (grids/A): 1.898329 object centre (A): 32.78850 31.74450 34.31500 number of atom coordinates read : 2488 total number of charged atoms : 2354 net assigned charge : 1.000028 assigned positive charge : 367.2930 centred at (gu) : 85.53797 88.41669 91.02964 assigned negative charge : -366.2939 centred at (gu) : 85.26762 88.57297 90.59351 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73356 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23713 grid for indexing accessible points = 1.400000 m= 25371 mr = 49002 m= 4197 mr = 17899 m= 238 mr = 2539 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 33661 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 122 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 18500 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) : 0.6327764 object centre at (A) : 32.78850 31.74450 34.31500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5874906E-02 2.5172828E-04 midg,1,midg; midg,igrid,midg 1.2259945E-02 -1.0959378E-03 1,midg,midg; igrid,midg,midg 4.7600684E-03 3.7397806E-02 gauss-seidel spectral radius is 0.9986315 estimated iterations to convergence 214 setup time was (sec) 1.020000 now iterating at: 14:59:13 rms-change max change #iterations 4.089439 181.9962 at 10iterations 1.909593 65.80457 at 20iterations 0.8897228 32.88297 at 30iterations 0.4145826 14.24760 at 40iterations 0.1941594 7.258890 at 50iterations 9.0869717E-02 2.794075 at 60iterations 4.2259689E-02 1.303879 at 70iterations 1.9837832E-02 0.5939426 at 80iterations 9.3034087E-03 0.3084030 at 90iterations 4.3421309E-03 0.1381927 at 100iterations 2.0361783E-03 6.7831039E-02 at 110iterations 9.5357513E-04 3.0864716E-02 at 120iterations finished qdiffx linear iterations at : 14:59:29 total time elapsed so far: 14.01000 # loops : 120 mean,max change (kT/e) : 9.5357513E-04 3.0864716E-02 energy calculations done at 14.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.20000 DelPhi exited at 14:59:29 14.200u 0.515s 0:18.15 81.0% 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 Sat Oct 15 2011 at 14:59:29 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2488 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: 2.847494 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): 5.400000 60.17700 ymin,ymax (A): 7.645999 55.84300 zmin,zma (A): 6.185000 62.44500 x,y,z range (A): 54.77700 48.19700 56.26000 scale (grids/A): 2.847494 object centre (A): 32.78850 31.74450 34.31500 number of atom coordinates read : 2488 total number of charged atoms : 2354 net assigned charge : 1.000028 assigned positive charge : 367.2930 centred at (gu) : 83.30692 87.62481 91.54427 assigned negative charge : -366.2939 centred at (gu) : 82.90131 87.85941 90.89029 start vw surface at 0.1200000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 169583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23713 grid for indexing accessible points = 1.400000 m= 81558 mr = 119476 m= 29668 mr = 64834 m= 7447 mr = 23028 m= 989 mr = 5438 m= 49 mr = 573 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.630000 number of dielectric boundary points 75931 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.850000 number of grid points assigned charge 18832 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) : 1.898329 object centre at (A) : 32.78850 31.74450 34.31500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8973372 2.8430356E-02 midg,1,midg; midg,igrid,midg 0.1163232 -3.8113620E-02 1,midg,midg; igrid,midg,midg 0.2375093 0.5573655 gauss-seidel spectral radius is 0.9992671 estimated iterations to convergence 292 setup time was (sec) 2.080000 now iterating at: 14:59:32 rms-change max change #iterations 9.720108 385.4418 at 10iterations 5.680463 143.6739 at 20iterations 3.304309 67.57618 at 30iterations 1.916861 39.82667 at 40iterations 1.110436 24.57086 at 50iterations 0.6409062 12.37799 at 60iterations 0.3711967 6.930984 at 70iterations 0.2146877 3.880372 at 80iterations 0.1236345 2.303969 at 90iterations 7.1270689E-02 1.334955 at 100iterations 4.1165154E-02 0.7290955 at 110iterations 2.3704262E-02 0.4616165 at 120iterations 1.3657100E-02 0.2476330 at 130iterations 7.8696683E-03 0.1532516 at 140iterations 4.5409654E-03 9.0402603E-02 at 150iterations 2.6210130E-03 5.5532455E-02 at 160iterations 1.5100574E-03 2.8680801E-02 at 170iterations 8.7396521E-04 1.6834259E-02 at 180iterations finished qdiffx linear iterations at : 15:00:02 total time elapsed so far: 22.50000 # loops : 180 mean,max change (kT/e) : 8.7396521E-04 1.6834259E-02 energy calculations done at 22.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.67000 DelPhi exited at 15:00:03 22.676u 0.608s 0:33.63 69.1% 0+0k 0+0io 0pf+0w