Sun Oct 9 07:30:24 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 Sun Oct 9 2011 at 07:30:24 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 = 2406 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5903912 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): -6.732000 52.97500 ymin,ymax (A): 20.04900 70.63300 zmin,zma (A): 51.21000 111.5090 x,y,z range (A): 59.70700 50.58400 60.29900 scale (grids/A): 0.5903912 object centre (A): 23.12150 45.34100 81.35950 number of atom coordinates read : 2406 total number of charged atoms : 2261 net assigned charge : -12.49998 assigned positive charge : 359.8441 centred at (gu) : 88.82923 90.84432 87.11386 assigned negative charge : -372.3444 centred at (gu) : 88.77242 91.22672 86.93977 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5576 nv = 96 ne = 84 npr = 47208 no. pairs analyzed = 47208 no. exposed pairs = 3406 no. arc points = 24514 no. surface atoms = 1138 nbur = 1268 mkacc time = 9.9999994E-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 = 1.456000 m= 259 mr = 2634 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2700000 number of dielectric boundary points 3185 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2405 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6907 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5869222E-08 3.3527081E-10 midg,1,midg; midg,igrid,midg 4.6940278E-09 -1.6749082E-08 1,midg,midg; igrid,midg,midg -6.5554202E-09 -1.6617596E-09 gauss-seidel spectral radius is 0.9851510 estimated iterations to convergence 67 setup time was (sec) 0.4800000 now iterating at: 07:30:25 rms-change max change #iterations 9.4488427E-02 18.76054 at 10iterations 7.5954697E-03 1.406580 at 20iterations 6.1385176E-04 0.1097012 at 30iterations 5.0149414E-05 1.0253906E-02 at 40iterations 4.1010649E-06 6.2274933E-04 at 50iterations finished qdiffx linear iterations at : 07:30:27 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 4.1010649E-06 6.2274933E-04 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 07:30:27 3.095u 0.160s 0:03.52 92.3% 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 07:30:27 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 = 2406 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.771174 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): -6.732000 52.97500 ymin,ymax (A): 20.04900 70.63300 zmin,zma (A): 51.21000 111.5090 x,y,z range (A): 59.70700 50.58400 60.29900 scale (grids/A): 1.771174 object centre (A): 23.12150 45.34100 81.35950 number of atom coordinates read : 2406 total number of charged atoms : 2261 net assigned charge : -12.49998 assigned positive charge : 359.8441 centred at (gu) : 86.48721 92.53248 81.34112 assigned negative charge : -372.3444 centred at (gu) : 86.31712 93.67993 80.81894 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59444 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24514 grid for indexing accessible points = 1.400000 m= 18734 mr = 36807 m= 2347 mr = 12776 m= 102 mr = 1343 m= 0 mr = 29 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 1008 time to turn everything in is 0.4300000 number of dielectric boundary points 29672 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 186 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 17594 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) : 0.5903912 object centre at (A) : 23.12150 45.34100 81.35950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0477425E-02 1.1444273E-02 midg,1,midg; midg,igrid,midg 4.2203080E-04 -4.8044041E-02 1,midg,midg; igrid,midg,midg -3.2022536E-02 -2.4141468E-02 gauss-seidel spectral radius is 0.9984019 estimated iterations to convergence 198 setup time was (sec) 0.7100000 now iterating at: 07:30:28 rms-change max change #iterations 3.538620 176.3463 at 10iterations 1.545952 81.32874 at 20iterations 0.6814566 25.54590 at 30iterations 0.2980343 11.08480 at 40iterations 0.1305633 4.752779 at 50iterations 5.7318605E-02 2.072435 at 60iterations 2.5145406E-02 0.9264565 at 70iterations 1.1036029E-02 0.3938904 at 80iterations 4.8509673E-03 0.1824646 at 90iterations 2.1231715E-03 7.5626373E-02 at 100iterations 9.2916767E-04 3.1893253E-02 at 110iterations 4.1016814E-04 1.4982224E-02 at 120iterations finished qdiffx linear iterations at : 07:30:35 total time elapsed so far: 7.120000 # loops : 120 mean,max change (kT/e) : 4.1016814E-04 1.4982224E-02 energy calculations done at 7.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 07:30:35 7.296u 0.187s 0:07.77 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 Sun Oct 9 2011 at 07:30:35 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 = 2406 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.656760 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): -6.732000 52.97500 ymin,ymax (A): 20.04900 70.63300 zmin,zma (A): 51.21000 111.5090 x,y,z range (A): 59.70700 50.58400 60.29900 scale (grids/A): 2.656760 object centre (A): 23.12150 45.34100 81.35950 number of atom coordinates read : 2406 total number of charged atoms : 2261 net assigned charge : -12.49998 assigned positive charge : 359.8441 centred at (gu) : 84.73071 93.79873 77.01161 assigned negative charge : -372.3444 centred at (gu) : 84.47560 95.51978 76.22839 start vw surface at 0.1400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 137303 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24514 grid for indexing accessible points = 1.400000 m= 62133 mr = 90385 m= 20083 mr = 48193 m= 3926 mr = 15311 m= 422 mr = 2764 m= 18 mr = 251 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 3551 time to turn everything in is 1.030000 number of dielectric boundary points 66975 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 18082 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) : 1.771174 object centre at (A) : 23.12150 45.34100 81.35950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3518889 0.1724148 midg,1,midg; midg,igrid,midg 3.2480869E-02 -0.5334066 1,midg,midg; igrid,midg,midg -0.1703627 -0.3463474 gauss-seidel spectral radius is 0.9992038 estimated iterations to convergence 280 setup time was (sec) 1.330000 now iterating at: 07:30:37 rms-change max change #iterations 8.867222 286.7829 at 10iterations 5.119700 156.2880 at 20iterations 2.905683 83.50302 at 30iterations 1.653047 38.07994 at 40iterations 0.9379991 24.10543 at 50iterations 0.5287324 12.88175 at 60iterations 0.2994262 6.171811 at 70iterations 0.1687553 3.620309 at 80iterations 9.5239356E-02 1.913263 at 90iterations 5.3522050E-02 1.310112 at 100iterations 3.0126192E-02 0.6300421 at 110iterations 1.6925732E-02 0.3565369 at 120iterations 9.5358975E-03 0.2025050 at 130iterations 5.3483448E-03 0.1368413 at 140iterations 3.0073330E-03 6.1075211E-02 at 150iterations 1.6916379E-03 3.6247253E-02 at 160iterations 9.4639248E-04 1.9524574E-02 at 170iterations 5.3172483E-04 1.0679722E-02 at 180iterations finished qdiffx linear iterations at : 07:30:47 total time elapsed so far: 11.45000 # loops : 180 mean,max change (kT/e) : 5.3172483E-04 1.0679722E-02 energy calculations done at 11.45000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.63000 DelPhi exited at 07:30:47 11.628u 0.190s 0:12.08 97.7% 0+0k 0+0io 0pf+0w