Tue Oct 11 08:05:40 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 08:05:40 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 = 3100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5466158 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): -20.89400 42.93000 ymin,ymax (A): -1.877000 63.25100 zmin,zma (A): 7.061000 55.66100 x,y,z range (A): 63.82400 65.12801 48.60000 scale (grids/A): 0.5466158 object centre (A): 11.01800 30.68700 31.36100 number of atom coordinates read : 3100 total number of charged atoms : 2953 net assigned charge : 9.500022 assigned positive charge : 461.5157 centred at (gu) : 89.87859 90.86990 89.57494 assigned negative charge : -452.0171 centred at (gu) : 89.76512 90.91295 89.61928 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6207 nv = 96 ne = 84 npr = 58214 no. pairs analyzed = 58214 no. exposed pairs = 4389 no. arc points = 31738 no. surface atoms = 1472 nbur = 1628 mkacc time = 0.1300000 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 = 1.568000 m= 251 mr = 2894 m= 0 mr = 3 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.3300000 number of dielectric boundary points 3561 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3154 ## 418 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0143221E-09 2.7309577E-10 midg,1,midg; midg,igrid,midg 7.3324091E-10 3.7831369E-10 1,midg,midg; igrid,midg,midg -1.9365351E-10 1.3422556E-09 gauss-seidel spectral radius is 0.9827717 estimated iterations to convergence 63 setup time was (sec) 0.5500000 now iterating at: 08:05:41 rms-change max change #iterations 7.2372645E-02 12.61407 at 10iterations 4.8093130E-03 0.7454834 at 20iterations 3.2493443E-04 4.9579620E-02 at 30iterations 2.2648366E-05 4.2295456E-03 at 40iterations 1.7276242E-06 2.5463104E-04 at 50iterations finished qdiffx linear iterations at : 08:05:43 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 1.7276242E-06 2.5463104E-04 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.210000 DelPhi exited at 08:05:44 3.212u 0.160s 0:04.03 83.6% 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 Tue Oct 11 2011 at 08:05:44 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 = 3100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.639848 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): -20.89400 42.93000 ymin,ymax (A): -1.877000 63.25100 zmin,zma (A): 7.061000 55.66100 x,y,z range (A): 63.82400 65.12801 48.60000 scale (grids/A): 1.639848 object centre (A): 11.01800 30.68700 31.36100 number of atom coordinates read : 3100 total number of charged atoms : 2953 net assigned charge : 9.500022 assigned positive charge : 461.5157 centred at (gu) : 89.63465 92.60860 88.72359 assigned negative charge : -452.0171 centred at (gu) : 89.29494 92.73824 88.85757 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68203 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31738 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19810 mr = 42940 m= 1921 mr = 13047 m= 50 mr = 843 m= 0 mr = 2 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 381 time to turn everything in is 0.4900000 number of dielectric boundary points 33152 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 370 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 22645 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) : 0.5466158 object centre at (A) : 11.01800 30.68700 31.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.1261666E-03 6.2879166E-03 midg,1,midg; midg,igrid,midg -4.7716848E-03 -1.1318914E-02 1,midg,midg; igrid,midg,midg 1.0530917E-03 2.3655511E-02 gauss-seidel spectral radius is 0.9982302 estimated iterations to convergence 189 setup time was (sec) 0.7500000 now iterating at: 08:05:45 rms-change max change #iterations 3.380543 152.5649 at 10iterations 1.410516 53.64298 at 20iterations 0.5899503 22.96451 at 30iterations 0.2485920 9.184931 at 40iterations 0.1046385 3.908607 at 50iterations 4.3816164E-02 1.533649 at 60iterations 1.8426159E-02 0.6582136 at 70iterations 7.7600270E-03 0.2746506 at 80iterations 3.2622176E-03 0.1263900 at 90iterations 1.3711316E-03 4.7328949E-02 at 100iterations 5.7732698E-04 1.9704819E-02 at 110iterations 2.4172918E-04 8.6975098E-03 at 120iterations finished qdiffx linear iterations at : 08:05:51 total time elapsed so far: 6.720000 # loops : 120 mean,max change (kT/e) : 2.4172918E-04 8.6975098E-03 energy calculations done at 6.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 08:05:52 6.897u 0.167s 0:07.57 93.1% 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 08:05:52 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 = 3100 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.459771 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): -20.89400 42.93000 ymin,ymax (A): -1.877000 63.25100 zmin,zma (A): 7.061000 55.66100 x,y,z range (A): 63.82400 65.12801 48.60000 scale (grids/A): 2.459771 object centre (A): 11.01800 30.68700 31.36100 number of atom coordinates read : 3100 total number of charged atoms : 2953 net assigned charge : 9.500022 assigned positive charge : 461.5157 centred at (gu) : 89.45183 93.91257 88.08523 assigned negative charge : -452.0171 centred at (gu) : 88.94242 94.10730 88.28619 start vw surface at 0.2100000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 158568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31738 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 68633 mr = 106264 m= 19059 mr = 52380 m= 2858 mr = 13948 m= 197 mr = 1786 m= 3 mr = 71 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 1290 time to turn everything in is 1.170000 number of dielectric boundary points 74869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 23601 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) : 1.639848 object centre at (A) : 11.01800 30.68700 31.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2634305E-02 8.7050751E-02 midg,1,midg; midg,igrid,midg -0.1055830 -6.9053903E-02 1,midg,midg; igrid,midg,midg 2.7076298E-02 0.3140906 gauss-seidel spectral radius is 0.9991629 estimated iterations to convergence 273 setup time was (sec) 1.450000 now iterating at: 08:05:53 rms-change max change #iterations 8.858294 282.1917 at 10iterations 5.042876 127.1380 at 20iterations 2.861101 88.11168 at 30iterations 1.610351 37.50632 at 40iterations 0.9020399 25.27218 at 50iterations 0.5040944 10.73918 at 60iterations 0.2804750 6.096436 at 70iterations 0.1564004 3.158855 at 80iterations 8.6753912E-02 1.848499 at 90iterations 4.8116889E-02 0.9797859 at 100iterations 2.6764194E-02 0.5311661 at 110iterations 1.4764760E-02 0.2841797 at 120iterations 8.2212528E-03 0.1640844 at 130iterations 4.5561451E-03 8.7226868E-02 at 140iterations 2.5201205E-03 5.2658081E-02 at 150iterations 1.3961572E-03 3.0136108E-02 at 160iterations 7.7463436E-04 1.5203476E-02 at 170iterations 4.2795748E-04 8.2931519E-03 at 180iterations finished qdiffx linear iterations at : 08:06:03 total time elapsed so far: 10.85000 # loops : 180 mean,max change (kT/e) : 4.2795748E-04 8.2931519E-03 energy calculations done at 10.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.03000 DelPhi exited at 08:06:03 11.037u 0.171s 0:11.74 95.4% 0+0k 0+0io 0pf+0w