Mon Oct 10 11:51:34 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 11:51:34 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2153 !!! WARNING: SEP 36 has a net charge of -0.4750 !!! WARNING: GLU 207 has a net charge of -2.0000 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: 0.5785890 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): -2.911000 42.25800 ymin,ymax (A): 19.86800 67.16400 zmin,zma (A): -22.87900 38.65000 x,y,z range (A): 45.16900 47.29600 61.52900 scale (grids/A): 0.5785890 object centre (A): 19.67350 43.51600 7.885501 number of atom coordinates read : 2153 total number of charged atoms : 2013 net assigned charge : -7.474989 assigned positive charge : 323.4319 centred at (gu) : 90.77631 89.83004 88.32928 assigned negative charge : -330.9069 centred at (gu) : 90.68801 89.81722 88.34916 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4495 nv = 96 ne = 84 npr = 45126 no. pairs analyzed = 45126 no. exposed pairs = 2695 no. arc points = 19074 no. surface atoms = 911 nbur = 1242 mkacc time = 0.1200000 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 = 1.484000 m= 196 mr = 2276 m= 0 mr = 6 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 19 time to turn everything in is 0.2700000 number of dielectric boundary points 2409 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1934 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 5842 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.8356395E-09 -1.2842638E-09 midg,1,midg; midg,igrid,midg -1.8361579E-09 -1.3152193E-09 1,midg,midg; igrid,midg,midg -2.4700262E-09 -2.2907792E-10 gauss-seidel spectral radius is 0.9845109 estimated iterations to convergence 66 setup time was (sec) 0.5300000 now iterating at: 11:51:35 rms-change max change #iterations 8.0808930E-02 15.04576 at 10iterations 6.2241890E-03 1.318161 at 20iterations 4.8405339E-04 8.7921143E-02 at 30iterations 3.7271275E-05 6.7508221E-03 at 40iterations 2.8440552E-06 4.9495697E-04 at 50iterations finished qdiffx linear iterations at : 11:51:39 total time elapsed so far: 4.780000 # loops : 50 mean,max change (kT/e) : 2.8440552E-06 4.9495697E-04 energy calculations done at 4.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.970000 DelPhi exited at 11:51:40 4.971u 0.459s 0:05.73 94.5% 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 11:51:40 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2153 !!! WARNING: SEP 36 has a net charge of -0.4750 !!! WARNING: GLU 207 has a net charge of -2.0000 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: 1.735767 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): -2.911000 42.25800 ymin,ymax (A): 19.86800 67.16400 zmin,zma (A): -22.87900 38.65000 x,y,z range (A): 45.16900 47.29600 61.52900 scale (grids/A): 1.735767 object centre (A): 19.67350 43.51600 7.885501 number of atom coordinates read : 2153 total number of charged atoms : 2013 net assigned charge : -7.474989 assigned positive charge : 323.4319 centred at (gu) : 92.32858 89.48991 84.98760 assigned negative charge : -330.9069 centred at (gu) : 92.06382 89.45149 85.04746 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 49475 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19074 grid for indexing accessible points = 1.400000 m= 15323 mr = 32654 m= 1734 mr = 10568 m= 52 mr = 927 m= 0 mr = 6 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1060 time to turn everything in is 0.4300000 number of dielectric boundary points 22429 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 15589 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) : 0.5785890 object centre at (A) : 19.67350 43.51600 7.885501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4883741E-03 -3.0677211E-03 midg,1,midg; midg,igrid,midg -4.8273350E-03 -1.1539318E-02 1,midg,midg; igrid,midg,midg -1.0883225E-02 1.1124314E-03 gauss-seidel spectral radius is 0.9982999 estimated iterations to convergence 193 setup time was (sec) 0.7700000 now iterating at: 11:51:50 rms-change max change #iterations 3.173486 186.5993 at 10iterations 1.356302 60.75517 at 20iterations 0.5797580 24.42840 at 30iterations 0.2485123 10.07861 at 40iterations 0.1063480 4.457515 at 50iterations 4.5409951E-02 1.824005 at 60iterations 1.9555368E-02 0.7683640 at 70iterations 8.3683897E-03 0.3546524 at 80iterations 3.5887982E-03 0.1618550 at 90iterations 1.5350521E-03 5.7743073E-02 at 100iterations 6.5580377E-04 2.5219917E-02 at 110iterations 2.8168893E-04 1.0822296E-02 at 120iterations finished qdiffx linear iterations at : 11:52:01 total time elapsed so far: 11.59000 # loops : 120 mean,max change (kT/e) : 2.8168893E-04 1.0822296E-02 energy calculations done at 11.59000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.76000 DelPhi exited at 11:52:02 11.769u 0.548s 0:21.73 56.6% 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 Mon Oct 10 2011 at 11:52:02 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: 245 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2153 !!! WARNING: SEP 36 has a net charge of -0.4750 !!! WARNING: GLU 207 has a net charge of -2.0000 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: 2.603650 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): -2.911000 42.25800 ymin,ymax (A): 19.86800 67.16400 zmin,zma (A): -22.87900 38.65000 x,y,z range (A): 45.16900 47.29600 61.52900 scale (grids/A): 2.603650 object centre (A): 19.67350 43.51600 7.885501 number of atom coordinates read : 2153 total number of charged atoms : 2013 net assigned charge : -7.474989 assigned positive charge : 323.4319 centred at (gu) : 93.49284 89.23489 82.48133 assigned negative charge : -330.9069 centred at (gu) : 93.09566 89.17718 82.57117 start vw surface at 0.1000000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 114531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19074 grid for indexing accessible points = 1.400000 m= 52058 mr = 79653 m= 15455 mr = 41105 m= 2845 mr = 11652 m= 251 mr = 2010 m= 3 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 3578 time to turn everything in is 1.040000 number of dielectric boundary points 50604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 16095 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) : 1.735767 object centre at (A) : 19.67350 43.51600 7.885501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5275605E-02 1.3146496E-02 midg,1,midg; midg,igrid,midg -2.7258433E-02 -0.1341807 1,midg,midg; igrid,midg,midg -0.1460162 3.9004218E-02 gauss-seidel spectral radius is 0.9991454 estimated iterations to convergence 270 setup time was (sec) 1.390000 now iterating at: 11:52:04 rms-change max change #iterations 7.853222 283.9368 at 10iterations 4.373047 109.2412 at 20iterations 2.419832 75.13535 at 30iterations 1.334044 28.46771 at 40iterations 0.7350070 17.99245 at 50iterations 0.4039320 8.948391 at 60iterations 0.2221478 5.127810 at 70iterations 0.1221718 2.763615 at 80iterations 6.7278326E-02 1.545959 at 90iterations 3.7001520E-02 0.9412413 at 100iterations 2.0333037E-02 0.5045013 at 110iterations 1.1182741E-02 0.2739582 at 120iterations 6.1383462E-03 0.1394196 at 130iterations 3.3774043E-03 7.6648235E-02 at 140iterations 1.8530415E-03 4.3304443E-02 at 150iterations 1.0188788E-03 2.4663925E-02 at 160iterations 5.6117051E-04 1.2432098E-02 at 170iterations 3.0849173E-04 7.6065063E-03 at 180iterations finished qdiffx linear iterations at : 11:52:21 total time elapsed so far: 18.42000 # loops : 180 mean,max change (kT/e) : 3.0849173E-04 7.6065063E-03 energy calculations done at 18.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.59000 DelPhi exited at 11:52:22 18.595u 0.556s 0:19.78 96.7% 0+0k 0+0io 0pf+0w