Sat Oct 15 13:46:00 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 13:46:00 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 = 2296 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: 0.6145454 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): -6.148000 39.61600 ymin,ymax (A): 14.02500 71.95400 zmin,zma (A): -0.7990000 48.52400 x,y,z range (A): 45.76400 57.92900 49.32300 scale (grids/A): 0.6145454 object centre (A): 16.73400 42.98950 23.86250 number of atom coordinates read : 2296 total number of charged atoms : 2217 net assigned charge : -1.999997 assigned positive charge : 337.9163 centred at (gu) : 90.39976 90.18066 88.23873 assigned negative charge : -339.9169 centred at (gu) : 90.43666 90.26202 88.17033 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5842 nv = 96 ne = 84 npr = 46073 no. pairs analyzed = 46073 no. exposed pairs = 3056 no. arc points = 21226 no. surface atoms = 1033 nbur = 1263 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 302 mr = 3045 m= 0 mr = 22 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.1700000 number of dielectric boundary points 3077 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2170 ## 227 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7263 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9592168E-09 1.3876027E-09 midg,1,midg; midg,igrid,midg 2.6046274E-09 -5.5500755E-09 1,midg,midg; igrid,midg,midg 4.9398940E-10 -3.3897727E-09 gauss-seidel spectral radius is 0.9862689 estimated iterations to convergence 70 setup time was (sec) 0.3700000 now iterating at: 13:46:01 rms-change max change #iterations 0.1096487 17.46402 at 10iterations 1.0007315E-02 1.652538 at 20iterations 9.4120426E-04 0.1308027 at 30iterations 1.1911189E-04 1.5754700E-02 at 40iterations 2.4170666E-05 3.3016205E-03 at 50iterations finished qdiffx linear iterations at : 13:46:04 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 2.4170666E-05 3.3016205E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 13:46:04 3.583u 0.216s 0:04.16 91.1% 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 Sat Oct 15 2011 at 13:46:04 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2296 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: 1.843636 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): -6.148000 39.61600 ymin,ymax (A): 14.02500 71.95400 zmin,zma (A): -0.7990000 48.52400 x,y,z range (A): 45.76400 57.92900 49.32300 scale (grids/A): 1.843636 object centre (A): 16.73400 42.98950 23.86250 number of atom coordinates read : 2296 total number of charged atoms : 2217 net assigned charge : -1.999997 assigned positive charge : 337.9163 centred at (gu) : 91.19897 90.54160 84.71572 assigned negative charge : -339.9169 centred at (gu) : 91.30986 90.78607 84.51093 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 63872 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21226 grid for indexing accessible points = 1.400000 m= 21757 mr = 43436 m= 3095 mr = 15227 m= 190 mr = 1774 m= 3 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 857 time to turn everything in is 0.3300000 number of dielectric boundary points 28431 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 17356 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) : 0.6145454 object centre at (A) : 16.73400 42.98950 23.86250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9497474E-02 9.9529000E-03 midg,1,midg; midg,igrid,midg 3.9458368E-02 -4.1334629E-03 1,midg,midg; igrid,midg,midg -3.2596595E-03 -1.9670777E-02 gauss-seidel spectral radius is 0.9985223 estimated iterations to convergence 206 setup time was (sec) 0.5700000 now iterating at: 13:46:05 rms-change max change #iterations 3.676466 186.4702 at 10iterations 1.665959 63.97490 at 20iterations 0.7584677 26.31411 at 30iterations 0.3444014 13.21554 at 40iterations 0.1567941 5.971924 at 50iterations 7.1356200E-02 2.435010 at 60iterations 3.2289419E-02 1.088241 at 70iterations 1.4727165E-02 0.5405502 at 80iterations 6.7342962E-03 0.2232248 at 90iterations 3.0596687E-03 0.1003551 at 100iterations 1.3983649E-03 5.2484274E-02 at 110iterations 6.4088957E-04 2.1864176E-02 at 120iterations finished qdiffx linear iterations at : 13:46:13 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 6.4088957E-04 2.1864176E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.230000 DelPhi exited at 13:46:13 8.235u 0.237s 0:08.80 96.1% 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 Sat Oct 15 2011 at 13:46:13 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 = 2296 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: 2.765454 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): -6.148000 39.61600 ymin,ymax (A): 14.02500 71.95400 zmin,zma (A): -0.7990000 48.52400 x,y,z range (A): 45.76400 57.92900 49.32300 scale (grids/A): 2.765454 object centre (A): 16.73400 42.98950 23.86250 number of atom coordinates read : 2296 total number of charged atoms : 2217 net assigned charge : -1.999997 assigned positive charge : 337.9163 centred at (gu) : 91.79832 90.81221 82.07335 assigned negative charge : -339.9169 centred at (gu) : 91.96477 91.17908 81.76646 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 147778 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21226 grid for indexing accessible points = 1.400000 m= 71262 mr = 105626 m= 24347 mr = 56661 m= 5419 mr = 18812 m= 738 mr = 3899 m= 37 mr = 430 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 2893 time to turn everything in is 0.8200000 number of dielectric boundary points 64142 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 17734 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) : 1.843636 object centre at (A) : 16.73400 42.98950 23.86250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3880458 0.1622248 midg,1,midg; midg,igrid,midg 0.4423336 -1.7468585E-02 1,midg,midg; igrid,midg,midg -3.9937176E-02 -0.2014742 gauss-seidel spectral radius is 0.9992272 estimated iterations to convergence 284 setup time was (sec) 1.070000 now iterating at: 13:46:14 rms-change max change #iterations 8.844777 390.9835 at 10iterations 5.142873 114.4592 at 20iterations 2.967007 61.81862 at 30iterations 1.703023 35.91281 at 40iterations 0.9757214 20.49650 at 50iterations 0.5602817 11.32293 at 60iterations 0.3197063 6.320574 at 70iterations 0.1820185 3.618721 at 80iterations 0.1042325 2.186584 at 90iterations 5.9113599E-02 1.126534 at 100iterations 3.3729251E-02 0.6511440 at 110iterations 1.9194420E-02 0.4285526 at 120iterations 1.0901497E-02 0.1999187 at 130iterations 6.2133283E-03 0.1262248 at 140iterations 3.5393231E-03 7.5279236E-02 at 150iterations 2.0232294E-03 3.8684249E-02 at 160iterations 1.1626236E-03 2.2819519E-02 at 170iterations 6.7111466E-04 1.4126778E-02 at 180iterations finished qdiffx linear iterations at : 13:46:27 total time elapsed so far: 13.19000 # loops : 180 mean,max change (kT/e) : 6.7111466E-04 1.4126778E-02 energy calculations done at 13.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.32000 DelPhi exited at 13:46:27 13.320u 0.271s 0:13.95 97.4% 0+0k 0+0io 0pf+0w