Mon Oct 10 14:25:41 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 14:25:41 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 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: 0.5617179 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): 71.11600 124.4030 ymin,ymax (A): 9.452001 72.82900 zmin,zma (A): -8.855000 52.54500 x,y,z range (A): 53.28700 63.37700 61.40000 scale (grids/A): 0.5617179 object centre (A): 97.75950 41.14050 21.84500 number of atom coordinates read : 2792 total number of charged atoms : 2642 net assigned charge : -1.499993 assigned positive charge : 415.8946 centred at (gu) : 88.24828 90.14825 89.41143 assigned negative charge : -417.3955 centred at (gu) : 88.42332 90.24759 89.30869 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5795 nv = 96 ne = 84 npr = 54899 no. pairs analyzed = 54899 no. exposed pairs = 3836 no. arc points = 27396 no. surface atoms = 1289 nbur = 1503 mkacc time = 0.1400000 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 = 1.540000 m= 235 mr = 2740 m= 2 mr = 7 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 3285 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2799 ## 343 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7520 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5500072E-09 7.9856988E-10 midg,1,midg; midg,igrid,midg 8.5471596E-10 -1.3514251E-09 1,midg,midg; igrid,midg,midg 2.6196993E-09 -1.4174822E-09 gauss-seidel spectral radius is 0.9836453 estimated iterations to convergence 64 setup time was (sec) 0.6000000 now iterating at: 14:25:42 rms-change max change #iterations 8.0787353E-02 13.48250 at 10iterations 5.6274682E-03 0.8702393 at 20iterations 4.0341396E-04 7.9715729E-02 at 30iterations 2.9479044E-05 5.1507950E-03 at 40iterations 2.0864966E-06 3.8337708E-04 at 50iterations finished qdiffx linear iterations at : 14:25:46 total time elapsed so far: 4.650000 # loops : 50 mean,max change (kT/e) : 2.0864966E-06 3.8337708E-04 energy calculations done at 4.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.830000 DelPhi exited at 14:25:47 4.834u 0.395s 0:05.74 90.9% 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 14:25:47 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 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: 1.685154 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): 71.11600 124.4030 ymin,ymax (A): 9.452001 72.82900 zmin,zma (A): -8.855000 52.54500 x,y,z range (A): 53.28700 63.37700 61.40000 scale (grids/A): 1.685154 object centre (A): 97.75950 41.14050 21.84500 number of atom coordinates read : 2792 total number of charged atoms : 2642 net assigned charge : -1.499993 assigned positive charge : 415.8946 centred at (gu) : 84.74426 90.44412 88.23326 assigned negative charge : -417.3955 centred at (gu) : 85.26968 90.74258 87.92571 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 63395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27396 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 18821 mr = 40694 m= 1894 mr = 12194 m= 57 mr = 743 m= 0 mr = 1 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 30535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 297 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 20396 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) : 0.5617179 object centre at (A) : 97.75950 41.14050 21.84500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0498819E-03 1.4567402E-02 midg,1,midg; midg,igrid,midg 2.3576468E-02 3.9347482E-04 1,midg,midg; igrid,midg,midg 1.0666706E-02 -1.5538361E-02 gauss-seidel spectral radius is 0.9982861 estimated iterations to convergence 192 setup time was (sec) 0.9100000 now iterating at: 14:25:48 rms-change max change #iterations 3.439948 207.7511 at 10iterations 1.459001 66.05990 at 20iterations 0.6233267 26.03076 at 30iterations 0.2652090 9.801776 at 40iterations 0.1128393 4.931656 at 50iterations 4.8083119E-02 1.822853 at 60iterations 2.0586243E-02 0.6961517 at 70iterations 8.7689813E-03 0.3379517 at 80iterations 3.7302512E-03 0.1291418 at 90iterations 1.5961879E-03 6.2111855E-02 at 100iterations 6.8166555E-04 2.4221897E-02 at 110iterations 2.9076668E-04 1.0826111E-02 at 120iterations finished qdiffx linear iterations at : 14:25:58 total time elapsed so far: 10.81000 # loops : 120 mean,max change (kT/e) : 2.9076668E-04 1.0826111E-02 energy calculations done at 10.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.98000 DelPhi exited at 14:25:59 10.981u 0.453s 0:12.18 93.8% 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 14:25:59 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: 301 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2792 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: 2.527731 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): 71.11600 124.4030 ymin,ymax (A): 9.452001 72.82900 zmin,zma (A): -8.855000 52.54500 x,y,z range (A): 53.28700 63.37700 61.40000 scale (grids/A): 2.527731 object centre (A): 97.75950 41.14050 21.84500 number of atom coordinates read : 2792 total number of charged atoms : 2642 net assigned charge : -1.499993 assigned positive charge : 415.8946 centred at (gu) : 82.11626 90.66594 87.34995 assigned negative charge : -417.3955 centred at (gu) : 82.90447 91.11380 86.88854 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 147334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27396 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 64625 mr = 100254 m= 18163 mr = 49255 m= 2684 mr = 12921 m= 204 mr = 1512 m= 5 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 68990 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 21126 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) : 1.685154 object centre at (A) : 97.75950 41.14050 21.84500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2279672 0.2156236 midg,1,midg; midg,igrid,midg 0.3820677 -0.1379326 1,midg,midg; igrid,midg,midg 0.1098021 -0.2493566 gauss-seidel spectral radius is 0.9991702 estimated iterations to convergence 274 setup time was (sec) 1.640000 now iterating at: 14:26:01 rms-change max change #iterations 8.756312 314.4736 at 10iterations 4.960211 153.7105 at 20iterations 2.805013 72.43031 at 30iterations 1.573309 40.56888 at 40iterations 0.8827537 19.71954 at 50iterations 0.4917290 10.99691 at 60iterations 0.2741035 5.943356 at 70iterations 0.1528217 3.243385 at 80iterations 8.4838018E-02 1.747025 at 90iterations 4.7122817E-02 1.022523 at 100iterations 2.6237873E-02 0.5310533 at 110iterations 1.4556663E-02 0.2904091 at 120iterations 8.0673434E-03 0.1793041 at 130iterations 4.4914107E-03 0.1032171 at 140iterations 2.4869398E-03 5.1491737E-02 at 150iterations 1.3808667E-03 2.8341293E-02 at 160iterations 7.6683646E-04 1.7150879E-02 at 170iterations 4.2601067E-04 8.7614059E-03 at 180iterations finished qdiffx linear iterations at : 14:26:18 total time elapsed so far: 18.12000 # loops : 180 mean,max change (kT/e) : 4.2601067E-04 8.7614059E-03 energy calculations done at 18.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.29000 DelPhi exited at 14:26:18 18.295u 0.470s 0:19.25 97.4% 0+0k 0+0io 0pf+0w