Mon Oct 10 17:14:58 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 Mon Oct 10 2011 at 17:14:58 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 = 3020 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: 0.5519380 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): -28.38600 36.11400 ymin,ymax (A): -24.58400 23.64900 zmin,zma (A): -37.91700 9.094000 x,y,z range (A): 64.50000 48.23300 47.01100 scale (grids/A): 0.5519380 object centre (A): 3.864001 -0.4674997 -14.41150 number of atom coordinates read : 3020 total number of charged atoms : 2878 net assigned charge : -3.499967 assigned positive charge : 452.2228 centred at (gu) : 90.20960 90.05209 90.54544 assigned negative charge : -455.7241 centred at (gu) : 90.26143 90.17404 90.67760 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5935 nv = 96 ne = 84 npr = 60162 no. pairs analyzed = 60162 no. exposed pairs = 4062 no. arc points = 28532 no. surface atoms = 1363 nbur = 1657 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= 241 mr = 2899 m= 0 mr = 4 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3100000 number of dielectric boundary points 3273 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2882 ## 376 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7846 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.3197665E-10 -1.6096431E-09 midg,1,midg; midg,igrid,midg 7.4591189E-10 -1.3333975E-09 1,midg,midg; igrid,midg,midg 1.6348230E-10 -7.4493095E-10 gauss-seidel spectral radius is 0.9830805 estimated iterations to convergence 63 setup time was (sec) 0.5200000 now iterating at: 17:14:58 rms-change max change #iterations 7.5731173E-02 11.58941 at 10iterations 5.0929482E-03 0.8068886 at 20iterations 3.4836651E-04 6.0420990E-02 at 30iterations 2.3542789E-05 4.1313171E-03 at 40iterations 1.7267158E-06 2.5081635E-04 at 50iterations finished qdiffx linear iterations at : 17:15:01 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 1.7267158E-06 2.5081635E-04 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 17:15:01 3.178u 0.173s 0:03.73 89.5% 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 17:15:01 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 = 3020 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: 1.655814 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): -28.38600 36.11400 ymin,ymax (A): -24.58400 23.64900 zmin,zma (A): -37.91700 9.094000 x,y,z range (A): 64.50000 48.23300 47.01100 scale (grids/A): 1.655814 object centre (A): 3.864001 -0.4674997 -14.41150 number of atom coordinates read : 3020 total number of charged atoms : 2878 net assigned charge : -3.499967 assigned positive charge : 452.2228 centred at (gu) : 90.62823 90.15559 91.63583 assigned negative charge : -455.7241 centred at (gu) : 90.78397 90.52177 92.03226 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66159 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28532 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 19530 mr = 43514 m= 1943 mr = 12757 m= 59 mr = 841 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 146 time to turn everything in is 0.4700000 number of dielectric boundary points 30573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 334 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 22154 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) : 0.5519380 object centre at (A) : 3.864001 -0.4674997 -14.41150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3683145E-03 -6.9409329E-03 midg,1,midg; midg,igrid,midg 5.6385635E-03 -1.8172253E-02 1,midg,midg; igrid,midg,midg 5.9443375E-04 -1.6988005E-02 gauss-seidel spectral radius is 0.9982463 estimated iterations to convergence 190 setup time was (sec) 0.7400000 now iterating at: 17:15:02 rms-change max change #iterations 3.421896 145.7136 at 10iterations 1.435026 57.76444 at 20iterations 0.6081271 24.26607 at 30iterations 0.2559198 9.322889 at 40iterations 0.1084776 3.781184 at 50iterations 4.5962568E-02 1.664548 at 60iterations 1.9337153E-02 0.7772694 at 70iterations 8.1911674E-03 0.2985897 at 80iterations 3.4577460E-03 0.1206360 at 90iterations 1.4673932E-03 4.7388077E-02 at 100iterations 6.1884132E-04 2.2259712E-02 at 110iterations 2.6224111E-04 9.4470978E-03 at 120iterations finished qdiffx linear iterations at : 17:15:08 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 2.6224111E-04 9.4470978E-03 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 17:15:09 7.061u 0.195s 0:07.69 94.2% 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 17:15:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3020 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.483721 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): -28.38600 36.11400 ymin,ymax (A): -24.58400 23.64900 zmin,zma (A): -37.91700 9.094000 x,y,z range (A): 64.50000 48.23300 47.01100 scale (grids/A): 2.483721 object centre (A): 3.864001 -0.4674997 -14.41150 number of atom coordinates read : 3020 total number of charged atoms : 2878 net assigned charge : -3.499967 assigned positive charge : 452.2228 centred at (gu) : 90.94212 90.23331 92.45361 assigned negative charge : -455.7241 centred at (gu) : 91.17594 90.78275 93.04836 start vw surface at 0.1900000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 153766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28532 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67929 mr = 107120 m= 18512 mr = 52087 m= 2970 mr = 13481 m= 226 mr = 1813 m= 3 mr = 99 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 498 time to turn everything in is 1.160000 number of dielectric boundary points 68806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 22998 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) : 1.655814 object centre at (A) : 3.864001 -0.4674997 -14.41150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3654051E-02 -5.8715384E-02 midg,1,midg; midg,igrid,midg 9.9041514E-02 -0.2553842 1,midg,midg; igrid,midg,midg 5.5883348E-02 -0.3354823 gauss-seidel spectral radius is 0.9991654 estimated iterations to convergence 273 setup time was (sec) 1.450000 now iterating at: 17:15:11 rms-change max change #iterations 8.941477 288.4824 at 10iterations 5.051019 137.7202 at 20iterations 2.839994 66.73685 at 30iterations 1.595874 37.07818 at 40iterations 0.8897170 18.48924 at 50iterations 0.4980494 14.02996 at 60iterations 0.2771416 5.925829 at 70iterations 0.1539199 3.400375 at 80iterations 8.5638605E-02 2.348068 at 90iterations 4.7486328E-02 1.207097 at 100iterations 2.6353065E-02 0.5614939 at 110iterations 1.4633743E-02 0.3027043 at 120iterations 8.1013842E-03 0.1634369 at 130iterations 4.5044604E-03 8.9324951E-02 at 140iterations 2.4923666E-03 5.4151535E-02 at 150iterations 1.3834514E-03 3.0679703E-02 at 160iterations 7.6673110E-04 1.6193390E-02 at 170iterations 4.2502480E-04 8.4705353E-03 at 180iterations finished qdiffx linear iterations at : 17:15:20 total time elapsed so far: 11.01000 # loops : 180 mean,max change (kT/e) : 4.2502480E-04 8.4705353E-03 energy calculations done at 11.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.19000 DelPhi exited at 17:15:21 11.191u 0.230s 0:11.74 97.2% 0+0k 0+0io 0pf+0w