Mon Oct 10 19:32:28 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 19:32:28 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 = 2694 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: 0.5751676 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): -10.64600 38.02300 ymin,ymax (A): -7.048000 46.47400 zmin,zma (A): -10.40400 51.49100 x,y,z range (A): 48.66900 53.52200 61.89500 scale (grids/A): 0.5751676 object centre (A): 13.68850 19.71300 20.54350 number of atom coordinates read : 2694 total number of charged atoms : 2556 net assigned charge : 4.000019 assigned positive charge : 396.4807 centred at (gu) : 91.01637 91.09338 90.74450 assigned negative charge : -392.4818 centred at (gu) : 90.95103 91.21044 90.70625 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5941 nv = 96 ne = 84 npr = 53088 no. pairs analyzed = 53088 no. exposed pairs = 3811 no. arc points = 26706 no. surface atoms = 1252 nbur = 1442 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 = 1.512000 m= 274 mr = 2865 m= 0 mr = 8 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2651 ## 308 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7552 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7191949E-11 1.6336045E-09 midg,1,midg; midg,igrid,midg 2.0466546E-09 -1.5951767E-09 1,midg,midg; igrid,midg,midg -2.6168698E-10 2.3058051E-09 gauss-seidel spectral radius is 0.9843854 estimated iterations to convergence 66 setup time was (sec) 0.5800000 now iterating at: 19:32:28 rms-change max change #iterations 8.6237624E-02 14.83359 at 10iterations 6.6966796E-03 1.081007 at 20iterations 5.4977811E-04 8.9148283E-02 at 30iterations 5.5072138E-05 8.6965561E-03 at 40iterations 8.2754559E-06 1.5754700E-03 at 50iterations finished qdiffx linear iterations at : 19:32:31 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 8.2754559E-06 1.5754700E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 19:32:32 3.585u 0.155s 0:04.23 88.1% 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 Mon Oct 10 2011 at 19:32:32 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 = 2694 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.725503 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): -10.64600 38.02300 ymin,ymax (A): -7.048000 46.47400 zmin,zma (A): -10.40400 51.49100 x,y,z range (A): 48.66900 53.52200 61.89500 scale (grids/A): 1.725503 object centre (A): 13.68850 19.71300 20.54350 number of atom coordinates read : 2694 total number of charged atoms : 2556 net assigned charge : 4.000019 assigned positive charge : 396.4807 centred at (gu) : 93.04861 93.27983 92.23293 assigned negative charge : -392.4818 centred at (gu) : 92.85295 93.63114 92.11852 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 64499 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26706 grid for indexing accessible points = 1.400000 m= 21063 mr = 41762 m= 2575 mr = 14203 m= 75 mr = 1283 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 258 time to turn everything in is 0.5100000 number of dielectric boundary points 30965 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 255 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 19812 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) : 0.5751676 object centre at (A) : 13.68850 19.71300 20.54350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9879505E-02 2.6603341E-02 midg,1,midg; midg,igrid,midg 7.8830644E-03 -1.2373282E-02 1,midg,midg; igrid,midg,midg -1.8622127E-03 -1.7751000E-03 gauss-seidel spectral radius is 0.9983636 estimated iterations to convergence 196 setup time was (sec) 0.8300000 now iterating at: 19:32:33 rms-change max change #iterations 3.484715 181.9576 at 10iterations 1.502459 63.33430 at 20iterations 0.6535916 22.84530 at 30iterations 0.2848462 11.90240 at 40iterations 0.1237525 4.620628 at 50iterations 5.3670779E-02 1.840628 at 60iterations 2.3435283E-02 0.8381653 at 70iterations 1.0181110E-02 0.4016868 at 80iterations 4.4369511E-03 0.1546288 at 90iterations 1.9422914E-03 7.5783849E-02 at 100iterations 8.4509910E-04 3.0261517E-02 at 110iterations 3.7004208E-04 1.5609741E-02 at 120iterations finished qdiffx linear iterations at : 19:32:41 total time elapsed so far: 8.540000 # loops : 120 mean,max change (kT/e) : 3.7004208E-04 1.5609741E-02 energy calculations done at 8.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.740000 DelPhi exited at 19:32:42 8.744u 0.200s 0:09.65 92.6% 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 19:32:42 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 = 2694 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.588254 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): -10.64600 38.02300 ymin,ymax (A): -7.048000 46.47400 zmin,zma (A): -10.40400 51.49100 x,y,z range (A): 48.66900 53.52200 61.89500 scale (grids/A): 2.588254 object centre (A): 13.68850 19.71300 20.54350 number of atom coordinates read : 2694 total number of charged atoms : 2556 net assigned charge : 4.000019 assigned positive charge : 396.4807 centred at (gu) : 94.57284 94.91962 93.34911 assigned negative charge : -392.4818 centred at (gu) : 94.27940 95.44666 93.17790 start vw surface at 0.1800000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 149546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26706 grid for indexing accessible points = 1.400000 m= 69619 mr = 102766 m= 22439 mr = 53866 m= 4222 mr = 16766 m= 332 mr = 2737 m= 2 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.6800000 no. cavity mid-points inaccessible to solvent = 905 time to turn everything in is 1.250000 number of dielectric boundary points 69901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 20425 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) : 1.725503 object centre at (A) : 13.68850 19.71300 20.54350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2229314 0.2449436 midg,1,midg; midg,igrid,midg 0.1557454 -8.1323594E-02 1,midg,midg; igrid,midg,midg -2.2060346E-02 -5.4563034E-02 gauss-seidel spectral radius is 0.9991976 estimated iterations to convergence 279 setup time was (sec) 1.580000 now iterating at: 19:32:43 rms-change max change #iterations 8.821594 312.0406 at 10iterations 5.066732 143.1294 at 20iterations 2.882688 77.23920 at 30iterations 1.639328 40.01681 at 40iterations 0.9296668 23.38467 at 50iterations 0.5231897 11.08748 at 60iterations 0.2951894 6.632814 at 70iterations 0.1664525 3.876972 at 80iterations 9.3843564E-02 1.880294 at 90iterations 5.2706085E-02 1.127716 at 100iterations 2.9577320E-02 0.6387882 at 110iterations 1.6607774E-02 0.3397408 at 120iterations 9.3364418E-03 0.1973267 at 130iterations 5.2285036E-03 0.1141434 at 140iterations 2.9364808E-03 5.8002472E-02 at 150iterations 1.6463801E-03 3.0590057E-02 at 160iterations 9.2256832E-04 1.9517899E-02 at 170iterations 5.1888678E-04 1.0861397E-02 at 180iterations finished qdiffx linear iterations at : 19:32:54 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 5.1888678E-04 1.0861397E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 19:32:55 12.904u 0.200s 0:13.64 96.0% 0+0k 0+0io 0pf+0w