Mon Oct 10 14:04:04 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+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 Mon Oct 10 2011 at 14:04:05 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6442972 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): -11.54600 39.35300 ymin,ymax (A): -23.57800 24.12900 zmin,zma (A): 0.6279999 55.88200 x,y,z range (A): 50.89899 47.70700 55.25400 scale (grids/A): 0.6442972 object centre (A): 13.90350 0.2754993 28.25500 number of atom coordinates read : 2559 total number of charged atoms : 2416 net assigned charge : 5.500009 assigned positive charge : 399.3647 centred at (gu) : 89.92648 90.09727 90.65968 assigned negative charge : -393.8653 centred at (gu) : 89.85978 89.95415 90.71951 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7133 nv = 96 ne = 84 npr = 50415 no. pairs analyzed = 50415 no. exposed pairs = 3310 no. arc points = 23377 no. surface atoms = 1098 nbur = 1461 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 3795 m= 2 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2900000 number of dielectric boundary points 3703 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2363 ## 276 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8542 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4821143E-08 1.1985775E-09 midg,1,midg; midg,igrid,midg -9.9916484E-09 2.8442555E-08 1,midg,midg; igrid,midg,midg 1.7666288E-10 1.7648649E-08 gauss-seidel spectral radius is 0.9875162 estimated iterations to convergence 73 setup time was (sec) 0.5500000 now iterating at: 14:04:05 rms-change max change #iterations 0.1490533 23.12663 at 10iterations 1.5595264E-02 2.171696 at 20iterations 1.7705305E-03 0.2873039 at 30iterations 2.7990568E-04 4.3937683E-02 at 40iterations 6.4949600E-05 9.5672607E-03 at 50iterations finished qdiffx linear iterations at : 14:04:08 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 6.4949600E-05 9.5672607E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 14:04:09 3.620u 0.208s 0:04.43 86.2% 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 Mon Oct 10 2011 at 14:04:09 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 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: 1.932892 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): -11.54600 39.35300 ymin,ymax (A): -23.57800 24.12900 zmin,zma (A): 0.6279999 55.88200 x,y,z range (A): 50.89899 47.70700 55.25400 scale (grids/A): 1.932892 object centre (A): 13.90350 0.2754993 28.25500 number of atom coordinates read : 2559 total number of charged atoms : 2416 net assigned charge : 5.500009 assigned positive charge : 399.3647 centred at (gu) : 89.77879 90.29105 91.97838 assigned negative charge : -393.8653 centred at (gu) : 89.57899 89.86221 92.15820 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 76211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23377 grid for indexing accessible points = 1.400000 m= 27018 mr = 51765 m= 4271 mr = 19325 m= 296 mr = 2468 m= 3 mr = 101 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1537 time to turn everything in is 0.6300000 number of dielectric boundary points 34140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 228 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 19025 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) : 0.6442972 object centre at (A) : 13.90350 0.2754993 28.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9162811E-02 5.3753895E-03 midg,1,midg; midg,igrid,midg -9.8450305E-03 1.8809631E-02 1,midg,midg; igrid,midg,midg 3.1787606E-03 6.1300155E-03 gauss-seidel spectral radius is 0.9986781 estimated iterations to convergence 218 setup time was (sec) 0.9600000 now iterating at: 14:04:10 rms-change max change #iterations 4.447246 185.1785 at 10iterations 2.103572 77.02283 at 20iterations 0.9948134 29.89566 at 30iterations 0.4696274 13.85457 at 40iterations 0.2235127 7.183442 at 50iterations 0.1060816 3.461573 at 60iterations 5.0116774E-02 1.561226 at 70iterations 2.3812171E-02 0.7402034 at 80iterations 1.1371884E-02 0.3889136 at 90iterations 5.4008756E-03 0.1672993 at 100iterations 2.5960610E-03 8.1843376E-02 at 110iterations 1.2537419E-03 4.1870117E-02 at 120iterations finished qdiffx linear iterations at : 14:04:17 total time elapsed so far: 7.460000 # loops : 120 mean,max change (kT/e) : 1.2537419E-03 4.1870117E-02 energy calculations done at 7.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 14:04:17 7.654u 0.200s 0:08.27 94.9% 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 Mon Oct 10 2011 at 14:04:17 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: 318 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 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: 2.899338 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): -11.54600 39.35300 ymin,ymax (A): -23.57800 24.12900 zmin,zma (A): 0.6279999 55.88200 x,y,z range (A): 50.89899 47.70700 55.25400 scale (grids/A): 2.899338 object centre (A): 13.90350 0.2754993 28.25500 number of atom coordinates read : 2559 total number of charged atoms : 2416 net assigned charge : 5.500009 assigned positive charge : 399.3647 centred at (gu) : 89.66808 90.43639 92.96745 assigned negative charge : -393.8653 centred at (gu) : 89.36835 89.79318 93.23726 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 176038 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23377 grid for indexing accessible points = 1.400000 m= 88033 mr = 125718 m= 30844 mr = 70756 m= 7364 mr = 24053 m= 1234 mr = 5159 m= 89 mr = 810 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 5660 time to turn everything in is 1.500000 number of dielectric boundary points 77072 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 19328 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) : 1.932892 object centre at (A) : 13.90350 0.2754993 28.25500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1932872 -7.4608997E-02 midg,1,midg; midg,igrid,midg -0.1633258 0.1984920 1,midg,midg; igrid,midg,midg 9.7940840E-02 -6.8548061E-03 gauss-seidel spectral radius is 0.9992705 estimated iterations to convergence 292 setup time was (sec) 1.860000 now iterating at: 14:04:19 rms-change max change #iterations 10.49915 430.2871 at 10iterations 6.234349 154.3837 at 20iterations 3.655548 76.10699 at 30iterations 2.147668 42.71069 at 40iterations 1.253772 24.91162 at 50iterations 0.7293124 12.88725 at 60iterations 0.4250006 8.361725 at 70iterations 0.2470060 4.880997 at 80iterations 0.1432209 2.881851 at 90iterations 8.2955919E-02 1.485489 at 100iterations 4.8052233E-02 0.8519716 at 110iterations 2.7857963E-02 0.5530586 at 120iterations 1.6187767E-02 0.3193378 at 130iterations 9.4420649E-03 0.1696835 at 140iterations 5.5493051E-03 0.1000862 at 150iterations 3.2981602E-03 5.6976318E-02 at 160iterations 2.0028080E-03 3.8248062E-02 at 170iterations 1.2481224E-03 2.4871826E-02 at 180iterations finished qdiffx linear iterations at : 14:04:31 total time elapsed so far: 12.95000 # loops : 180 mean,max change (kT/e) : 1.2481224E-03 2.4871826E-02 energy calculations done at 12.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.14000 DelPhi exited at 14:04:31 13.139u 0.260s 0:13.74 97.4% 0+0k 0+0io 0pf+0w