Tue Nov 22 14:20:47 PST 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 Tue Nov 22 2011 at 14:20:51 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6006107 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): -24.74200 34.53100 ymin,ymax (A): -19.13000 20.75300 zmin,zma (A): -4.640000 38.73100 x,y,z range (A): 59.27300 39.88300 43.37100 scale (grids/A): 0.6006107 object centre (A): 4.894502 0.8115005 17.04550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000011 assigned positive charge : 290.2520 centred at (gu) : 90.13572 90.30998 90.79921 assigned negative charge : -285.2523 centred at (gu) : 90.16537 90.41403 90.93446 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4756 nv = 96 ne = 84 npr = 39757 no. pairs analyzed = 39757 no. exposed pairs = 2607 no. arc points = 18506 no. surface atoms = 884 nbur = 1084 mkacc time = 8.0000006E-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= 252 mr = 2488 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.2200000 number of dielectric boundary points 2495 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1891 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5867 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9027444E-09 -1.8557729E-09 midg,1,midg; midg,igrid,midg 4.7013620E-09 -7.0040895E-10 1,midg,midg; igrid,midg,midg 2.9501201E-09 1.4619429E-09 gauss-seidel spectral radius is 0.9856012 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 14:20:55 rms-change max change #iterations 9.1841437E-02 20.84678 at 10iterations 7.5319083E-03 1.363535 at 20iterations 6.5648474E-04 0.1409454 at 30iterations 5.3627278E-05 9.6664429E-03 at 40iterations 4.7219582E-06 9.9945068E-04 at 50iterations finished qdiffx linear iterations at : 14:21:02 total time elapsed so far: 2.820000 # loops : 50 mean,max change (kT/e) : 4.7219582E-06 9.9945068E-04 energy calculations done at 2.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 2.990000 DelPhi exited at 14:21:03 2.997u 0.132s 0:12.06 25.8% 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 Tue Nov 22 2011 at 14:21:03 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.801832 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): -24.74200 34.53100 ymin,ymax (A): -19.13000 20.75300 zmin,zma (A): -4.640000 38.73100 x,y,z range (A): 59.27300 39.88300 43.37100 scale (grids/A): 1.801832 object centre (A): 4.894502 0.8115005 17.04550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000011 assigned positive charge : 290.2520 centred at (gu) : 90.40739 90.92985 92.39777 assigned negative charge : -285.2523 centred at (gu) : 90.49616 91.24223 92.80355 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 51298 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18506 grid for indexing accessible points = 1.400000 m= 18003 mr = 34033 m= 2644 mr = 13301 m= 99 mr = 1611 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 661 time to turn everything in is 0.3600000 number of dielectric boundary points 23080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 177 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 14345 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) : 0.6006107 object centre at (A) : 4.894502 0.8115005 17.04550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8558326E-03 -3.9944928E-03 midg,1,midg; midg,igrid,midg 7.4958471E-03 -1.4923242E-03 1,midg,midg; igrid,midg,midg 3.7825201E-02 2.3129810E-02 gauss-seidel spectral radius is 0.9984046 estimated iterations to convergence 199 setup time was (sec) 0.6200000 now iterating at: 14:21:05 rms-change max change #iterations 3.189067 185.6378 at 10iterations 1.398309 58.79497 at 20iterations 0.6157606 25.57030 at 30iterations 0.2711597 10.01121 at 40iterations 0.1183272 5.653461 at 50iterations 5.2218415E-02 2.019372 at 60iterations 2.3072522E-02 0.9658403 at 70iterations 1.0118751E-02 0.3865770 at 80iterations 4.4632433E-03 0.1739977 at 90iterations 1.9582557E-03 8.4622622E-02 at 100iterations 8.5881288E-04 3.2838702E-02 at 110iterations 3.7963263E-04 1.5460014E-02 at 120iterations finished qdiffx linear iterations at : 14:21:24 total time elapsed so far: 6.490000 # loops : 120 mean,max change (kT/e) : 3.7963263E-04 1.5460014E-02 energy calculations done at 6.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.670000 DelPhi exited at 14:21:25 6.673u 0.150s 0:22.26 30.6% 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 Tue Nov 22 2011 at 14:21:27 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1968 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.702748 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): -24.74200 34.53100 ymin,ymax (A): -19.13000 20.75300 zmin,zma (A): -4.640000 38.73100 x,y,z range (A): 59.27300 39.88300 43.37100 scale (grids/A): 2.702748 object centre (A): 4.894502 0.8115005 17.04550 number of atom coordinates read : 1968 total number of charged atoms : 1836 net assigned charge : 5.000011 assigned positive charge : 290.2520 centred at (gu) : 90.61105 91.39487 93.59660 assigned negative charge : -285.2523 centred at (gu) : 90.74442 91.86346 94.20541 start vw surface at 0.1200000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 118422 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18506 grid for indexing accessible points = 1.400000 m= 58614 mr = 82681 m= 20713 mr = 47581 m= 4544 mr = 16734 m= 430 mr = 3450 m= 11 mr = 240 m= 0 mr = 2 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 2249 time to turn everything in is 0.8900000 number of dielectric boundary points 52046 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 14682 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) : 1.801832 object centre at (A) : 4.894502 0.8115005 17.04550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2738700E-02 -1.9349599E-02 midg,1,midg; midg,igrid,midg 6.0087707E-02 -1.7033771E-02 1,midg,midg; igrid,midg,midg 0.3835082 0.1886389 gauss-seidel spectral radius is 0.9991792 estimated iterations to convergence 276 setup time was (sec) 1.160000 now iterating at: 14:21:33 rms-change max change #iterations 7.776689 255.7611 at 10iterations 4.427912 136.9778 at 20iterations 2.504689 57.86964 at 30iterations 1.406604 34.50100 at 40iterations 0.7894453 19.23808 at 50iterations 0.4416563 10.64812 at 60iterations 0.2471838 5.829815 at 70iterations 0.1376866 3.226687 at 80iterations 7.7117778E-02 1.710499 at 90iterations 4.2990196E-02 0.9937344 at 100iterations 2.3924448E-02 0.5227828 at 110iterations 1.3334782E-02 0.3276185 at 120iterations 7.4308002E-03 0.1692219 at 130iterations 4.1427366E-03 9.0313435E-02 at 140iterations 2.3073726E-03 4.8949242E-02 at 150iterations 1.2840555E-03 2.7770519E-02 at 160iterations 7.1445398E-04 1.4607430E-02 at 170iterations 3.9801758E-04 8.6495876E-03 at 180iterations finished qdiffx linear iterations at : 14:22:00 total time elapsed so far: 10.18000 # loops : 180 mean,max change (kT/e) : 3.9801758E-04 8.6495876E-03 energy calculations done at 10.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.37000 DelPhi exited at 14:22:01 10.371u 0.144s 0:35.12 29.9% 0+0k 0+0io 0pf+0w