Sat Oct 15 15:31:14 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 Sat Oct 15 2011 at 15:31:14 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7109336 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): 25.85500 72.49600 ymin,ymax (A): -18.48700 31.58800 zmin,zma (A): 4.281000 46.46000 x,y,z range (A): 46.64100 50.07500 42.17900 scale (grids/A): 0.7109336 object centre (A): 49.17550 6.550501 25.37050 number of atom coordinates read : 2327 total number of charged atoms : 1996 net assigned charge : 5.945011 assigned positive charge : 326.9459 centred at (gu) : 89.21621 90.09815 90.23272 assigned negative charge : -321.0010 centred at (gu) : 89.33627 90.03180 90.31223 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7269 nv = 96 ne = 84 npr = 42535 no. pairs analyzed = 42535 no. exposed pairs = 2588 no. arc points = 17459 no. surface atoms = 885 nbur = 1442 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 517 mr = 4216 m= 4 mr = 117 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1630 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8018 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3118629E-08 1.0261743E-08 midg,1,midg; midg,igrid,midg 1.7012233E-08 9.1959542E-08 1,midg,midg; igrid,midg,midg 1.3885081E-07 -1.0517687E-08 gauss-seidel spectral radius is 0.9896895 estimated iterations to convergence 80 setup time was (sec) 0.3800000 now iterating at: 15:31:15 rms-change max change #iterations 0.2096034 25.74719 at 10iterations 2.6348449E-02 3.556358 at 20iterations 3.6709118E-03 0.4688320 at 30iterations 6.3790154E-04 9.0648651E-02 at 40iterations 1.5832929E-04 1.8369675E-02 at 50iterations finished qdiffx linear iterations at : 15:31:18 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.5832929E-04 1.8369675E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 15:31:18 3.415u 0.153s 0:03.87 91.9% 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 15:31:18 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.132801 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): 25.85500 72.49600 ymin,ymax (A): -18.48700 31.58800 zmin,zma (A): 4.281000 46.46000 x,y,z range (A): 46.64100 50.07500 42.17900 scale (grids/A): 2.132801 object centre (A): 49.17550 6.550501 25.37050 number of atom coordinates read : 2327 total number of charged atoms : 1996 net assigned charge : 5.945011 assigned positive charge : 326.9459 centred at (gu) : 87.64864 90.29441 90.69803 assigned negative charge : -321.0010 centred at (gu) : 88.00898 90.09538 90.93679 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 77227 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17459 grid for indexing accessible points = 1.400000 m= 31799 mr = 55063 m= 6481 mr = 24454 m= 612 mr = 4426 m= 19 mr = 315 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 31880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 55 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 15855 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) : 0.7109336 object centre at (A) : 49.17550 6.550501 25.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9143702E-02 3.0327775E-02 midg,1,midg; midg,igrid,midg 4.4070724E-02 2.8732957E-02 1,midg,midg; igrid,midg,midg 4.2246155E-02 -5.1378150E-02 gauss-seidel spectral radius is 0.9988456 estimated iterations to convergence 233 setup time was (sec) 0.6200000 now iterating at: 15:31:19 rms-change max change #iterations 4.736731 205.7757 at 10iterations 2.358571 74.59190 at 20iterations 1.170377 35.64236 at 30iterations 0.5840289 18.99790 at 40iterations 0.2913405 9.597473 at 50iterations 0.1455180 4.806743 at 60iterations 7.2635330E-02 2.531219 at 70iterations 3.6380839E-02 0.9861679 at 80iterations 1.8253610E-02 0.5184650 at 90iterations 9.1933310E-03 0.2690129 at 100iterations 4.6852771E-03 0.1406660 at 110iterations 2.4558443E-03 7.5611115E-02 at 120iterations finished qdiffx linear iterations at : 15:31:27 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 2.4558443E-03 7.5611115E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 15:31:27 8.216u 0.191s 0:08.69 96.6% 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 15:31:27 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.199201 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): 25.85500 72.49600 ymin,ymax (A): -18.48700 31.58800 zmin,zma (A): 4.281000 46.46000 x,y,z range (A): 46.64100 50.07500 42.17900 scale (grids/A): 3.199201 object centre (A): 49.17550 6.550501 25.37050 number of atom coordinates read : 2327 total number of charged atoms : 1996 net assigned charge : 5.945011 assigned positive charge : 326.9459 centred at (gu) : 86.47274 90.44161 91.04692 assigned negative charge : -321.0010 centred at (gu) : 87.01347 90.14307 91.40523 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 178073 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17459 grid for indexing accessible points = 1.400000 m= 98145 mr = 132469 m= 40960 mr = 82161 m= 12311 mr = 33939 m= 2582 mr = 9760 m= 320 mr = 1911 m= 13 mr = 204 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 71960 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 15968 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) : 2.132801 object centre at (A) : 49.17550 6.550501 25.37050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8783553E-02 0.2415134 midg,1,midg; midg,igrid,midg 0.3641521 0.1504468 1,midg,midg; igrid,midg,midg 0.4015061 -0.6322636 gauss-seidel spectral radius is 0.9993005 estimated iterations to convergence 298 setup time was (sec) 1.510000 now iterating at: 15:31:29 rms-change max change #iterations 10.53092 386.2090 at 10iterations 6.238032 138.8107 at 20iterations 3.693323 72.25470 at 30iterations 2.180890 44.09579 at 40iterations 1.283527 24.63308 at 50iterations 0.7549824 13.61332 at 60iterations 0.4436503 7.734815 at 70iterations 0.2608582 4.687572 at 80iterations 0.1528819 2.745660 at 90iterations 8.9885361E-02 1.555945 at 100iterations 5.2656975E-02 0.9291019 at 110iterations 3.1147473E-02 0.5303717 at 120iterations 1.8471790E-02 0.3216019 at 130iterations 1.1137689E-02 0.2071686 at 140iterations 6.8382733E-03 0.1178703 at 150iterations 4.3613273E-03 7.8823090E-02 at 160iterations 2.9234430E-03 6.0241699E-02 at 170iterations 2.0839788E-03 3.7357330E-02 at 180iterations finished qdiffx linear iterations at : 15:31:40 total time elapsed so far: 12.87000 # loops : 180 mean,max change (kT/e) : 2.0839788E-03 3.7357330E-02 energy calculations done at 12.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.99000 DelPhi exited at 15:31:41 12.996u 0.343s 0:13.67 97.5% 0+0k 0+0io 0pf+0w