Sun Oct 9 23:42:17 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 Sun Oct 9 2011 at 23:42:17 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2815 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5417414 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): -40.67200 25.04200 ymin,ymax (A): -27.75100 23.85600 zmin,zma (A): -7.627000 36.51200 x,y,z range (A): 65.71400 51.60700 44.13900 scale (grids/A): 0.5417414 object centre (A): -7.815001 -1.947500 14.44250 number of atom coordinates read : 2815 total number of charged atoms : 2673 net assigned charge : 5.000008 assigned positive charge : 432.0916 centred at (gu) : 89.87908 90.02725 89.61612 assigned negative charge : -427.0925 centred at (gu) : 89.93546 90.11657 89.55589 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5361 nv = 96 ne = 84 npr = 54540 no. pairs analyzed = 54540 no. exposed pairs = 3775 no. arc points = 27963 no. surface atoms = 1251 nbur = 1564 mkacc time = 8.9999996E-02 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= 196 mr = 2545 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3006 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2851 ## 475 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7104 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.3459551E-11 5.3705040E-10 midg,1,midg; midg,igrid,midg 7.4101369E-10 -2.2852018E-10 1,midg,midg; igrid,midg,midg 5.8735117E-10 -4.2442879E-11 gauss-seidel spectral radius is 0.9824306 estimated iterations to convergence 62 setup time was (sec) 0.3900000 now iterating at: 23:42:18 rms-change max change #iterations 7.1197458E-02 13.09993 at 10iterations 4.5484169E-03 0.7721453 at 20iterations 2.9168397E-04 5.4313660E-02 at 30iterations 1.8909546E-05 3.4141541E-03 at 40iterations 1.2945335E-06 2.4414063E-04 at 50iterations finished qdiffx linear iterations at : 23:42:20 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 1.2945335E-06 2.4414063E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 23:42:21 3.426u 0.166s 0:04.03 88.8% 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 Sun Oct 9 2011 at 23:42:21 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2815 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.625224 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): -40.67200 25.04200 ymin,ymax (A): -27.75100 23.85600 zmin,zma (A): -7.627000 36.51200 x,y,z range (A): 65.71400 51.60700 44.13900 scale (grids/A): 1.625224 object centre (A): -7.815001 -1.947500 14.44250 number of atom coordinates read : 2815 total number of charged atoms : 2673 net assigned charge : 5.000008 assigned positive charge : 432.0916 centred at (gu) : 89.63697 90.08120 88.84765 assigned negative charge : -427.0925 centred at (gu) : 89.80626 90.34968 88.66749 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 59549 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27963 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 16918 mr = 38275 m= 1604 mr = 11007 m= 20 mr = 653 m= 0 mr = 2 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 677 time to turn everything in is 0.2900000 number of dielectric boundary points 28154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 363 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 20413 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) : 0.5417414 object centre at (A) : -7.815001 -1.947500 14.44250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4508973E-03 8.4428053E-04 midg,1,midg; midg,igrid,midg 9.6444441E-03 2.1426522E-03 1,midg,midg; igrid,midg,midg 1.4792502E-02 1.4967130E-03 gauss-seidel spectral radius is 0.9981543 estimated iterations to convergence 185 setup time was (sec) 0.5000000 now iterating at: 23:42:22 rms-change max change #iterations 3.199742 148.4886 at 10iterations 1.312657 53.20282 at 20iterations 0.5392011 21.51646 at 30iterations 0.2230227 9.097229 at 40iterations 9.1770560E-02 3.855303 at 50iterations 3.8015857E-02 1.384733 at 60iterations 1.5693981E-02 0.6193695 at 70iterations 6.4765387E-03 0.2505302 at 80iterations 2.6680122E-03 9.9874496E-02 at 90iterations 1.1016688E-03 4.2726517E-02 at 100iterations 4.5601797E-04 1.7659783E-02 at 110iterations 1.8846946E-04 6.8696737E-03 at 120iterations finished qdiffx linear iterations at : 23:42:29 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 1.8846946E-04 6.8696737E-03 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 23:42:29 7.645u 0.216s 0:08.29 94.6% 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 Sun Oct 9 2011 at 23:42:29 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2815 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.437836 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): -40.67200 25.04200 ymin,ymax (A): -27.75100 23.85600 zmin,zma (A): -7.627000 36.51200 x,y,z range (A): 65.71400 51.60700 44.13900 scale (grids/A): 2.437836 object centre (A): -7.815001 -1.947500 14.44250 number of atom coordinates read : 2815 total number of charged atoms : 2673 net assigned charge : 5.000008 assigned positive charge : 432.0916 centred at (gu) : 89.45531 90.12170 88.27116 assigned negative charge : -427.0925 centred at (gu) : 89.70936 90.52441 88.00108 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 138676 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27963 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 59161 mr = 94215 m= 15657 mr = 45481 m= 2306 mr = 11219 m= 97 mr = 1439 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 2237 time to turn everything in is 0.6900000 number of dielectric boundary points 63525 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 21356 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) : 1.625224 object centre at (A) : -7.815001 -1.947500 14.44250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0030220E-02 1.1747171E-02 midg,1,midg; midg,igrid,midg 0.1542681 8.1391573E-02 1,midg,midg; igrid,midg,midg 9.5389836E-02 -2.9515902E-02 gauss-seidel spectral radius is 0.9991245 estimated iterations to convergence 267 setup time was (sec) 0.9200000 now iterating at: 23:42:31 rms-change max change #iterations 8.222371 369.1720 at 10iterations 4.485747 128.8841 at 20iterations 2.465429 68.68122 at 30iterations 1.346772 29.38841 at 40iterations 0.7367505 16.56430 at 50iterations 0.4025039 9.113102 at 60iterations 0.2186217 4.868731 at 70iterations 0.1194131 2.882021 at 80iterations 6.5181389E-02 1.316439 at 90iterations 3.5557888E-02 0.8138514 at 100iterations 1.9319003E-02 0.4066925 at 110iterations 1.0561709E-02 0.2649460 at 120iterations 5.7557519E-03 0.1233306 at 130iterations 3.1424803E-03 7.0846558E-02 at 140iterations 1.7112126E-03 3.6610484E-02 at 150iterations 9.3338790E-04 2.3108959E-02 at 160iterations 5.0802593E-04 1.1373520E-02 at 170iterations 2.7808474E-04 6.1950684E-03 at 180iterations finished qdiffx linear iterations at : 23:42:42 total time elapsed so far: 11.95000 # loops : 180 mean,max change (kT/e) : 2.7808474E-04 6.1950684E-03 energy calculations done at 11.95000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.08000 DelPhi exited at 23:42:42 12.087u 0.219s 0:12.57 97.7% 0+0k 0+0io 0pf+0w