Sat Oct 8 18:23:36 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 Sat Oct 8 2011 at 18:23:36 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3390 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: 0.5399993 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): -49.64100 5.088000 ymin,ymax (A): -125.0080 -59.08200 zmin,zma (A): -16.53800 29.84700 x,y,z range (A): 54.72900 65.92601 46.38500 scale (grids/A): 0.5399993 object centre (A): -22.27650 -92.04500 6.654500 number of atom coordinates read : 3390 total number of charged atoms : 3244 net assigned charge : -4.999993 assigned positive charge : 510.5475 centred at (gu) : 90.18994 90.60867 89.75833 assigned negative charge : -515.5488 centred at (gu) : 90.11392 90.66402 89.76283 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6211 nv = 96 ne = 84 npr = 70156 no. pairs analyzed = 70156 no. exposed pairs = 4016 no. arc points = 28022 no. surface atoms = 1364 nbur = 2026 mkacc time = 0.2000000 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 = 1.624000 m= 216 mr = 3360 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.4200000 number of dielectric boundary points 3061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2785 ## 383 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8265 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2963699E-10 -2.5642699E-10 midg,1,midg; midg,igrid,midg 7.8764072E-11 -6.8366546E-10 1,midg,midg; igrid,midg,midg -6.8303535E-10 2.3007982E-10 gauss-seidel spectral radius is 0.9823462 estimated iterations to convergence 62 setup time was (sec) 0.6800000 now iterating at: 18:23:37 rms-change max change #iterations 7.6341942E-02 11.92347 at 10iterations 4.9655791E-03 0.8967705 at 20iterations 4.0273179E-04 8.1091881E-02 at 30iterations 5.7374651E-05 1.3507843E-02 at 40iterations 1.1837098E-05 3.0126572E-03 at 50iterations finished qdiffx linear iterations at : 18:23:40 total time elapsed so far: 4.030000 # loops : 50 mean,max change (kT/e) : 1.1837098E-05 3.0126572E-03 energy calculations done at 4.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 18:23:41 4.218u 0.292s 0:04.81 93.5% 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 Sat Oct 8 2011 at 18:23:41 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3390 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: 1.619998 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): -49.64100 5.088000 ymin,ymax (A): -125.0080 -59.08200 zmin,zma (A): -16.53800 29.84700 x,y,z range (A): 54.72900 65.92601 46.38500 scale (grids/A): 1.619998 object centre (A): -22.27650 -92.04500 6.654500 number of atom coordinates read : 3390 total number of charged atoms : 3244 net assigned charge : -4.999993 assigned positive charge : 510.5475 centred at (gu) : 90.56892 91.82525 89.27426 assigned negative charge : -515.5488 centred at (gu) : 90.34155 91.99173 89.28793 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 69976 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28022 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 20418 mr = 48903 m= 1861 mr = 13977 m= 41 mr = 868 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 988 time to turn everything in is 0.6300000 number of dielectric boundary points 28548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 367 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 24788 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) : 0.5399993 object centre at (A) : -22.27650 -92.04500 6.654500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.5536117E-03 -3.0482081E-03 midg,1,midg; midg,igrid,midg 1.6548418E-02 4.1647116E-03 1,midg,midg; igrid,midg,midg -9.9852942E-03 4.7034482E-03 gauss-seidel spectral radius is 0.9981841 estimated iterations to convergence 186 setup time was (sec) 0.9300000 now iterating at: 18:23:42 rms-change max change #iterations 3.502795 142.8595 at 10iterations 1.457722 57.42560 at 20iterations 0.6060512 22.93817 at 30iterations 0.2526882 8.383314 at 40iterations 0.1059790 3.899788 at 50iterations 4.4209685E-02 1.525606 at 60iterations 1.8448519E-02 0.6778927 at 70iterations 7.7210963E-03 0.2625999 at 80iterations 3.2425651E-03 0.1075134 at 90iterations 1.3647804E-03 4.6577454E-02 at 100iterations 5.7621353E-04 2.1718979E-02 at 110iterations 2.4737936E-04 8.4667206E-03 at 120iterations finished qdiffx linear iterations at : 18:23:50 total time elapsed so far: 9.300000 # loops : 120 mean,max change (kT/e) : 2.4737936E-04 8.4667206E-03 energy calculations done at 9.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.480000 DelPhi exited at 18:23:51 9.481u 0.308s 0:10.07 97.1% 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 Sat Oct 8 2011 at 18:23:51 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3390 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: 2.429997 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): -49.64100 5.088000 ymin,ymax (A): -125.0080 -59.08200 zmin,zma (A): -16.53800 29.84700 x,y,z range (A): 54.72900 65.92601 46.38500 scale (grids/A): 2.429997 object centre (A): -22.27650 -92.04500 6.654500 number of atom coordinates read : 3390 total number of charged atoms : 3244 net assigned charge : -4.999993 assigned positive charge : 510.5475 centred at (gu) : 90.85303 92.73744 88.91112 assigned negative charge : -515.5488 centred at (gu) : 90.51209 92.98737 88.93188 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 163119 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28022 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 73213 mr = 119828 m= 18853 mr = 58244 m= 2671 mr = 13771 m= 198 mr = 1656 m= 4 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 3435 time to turn everything in is 1.530000 number of dielectric boundary points 64471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 28 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 25908 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) : 1.619998 object centre at (A) : -22.27650 -92.04500 6.654500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1018740 -3.6870200E-02 midg,1,midg; midg,igrid,midg 0.4688201 0.3312979 1,midg,midg; igrid,midg,midg -0.1325774 8.6361252E-02 gauss-seidel spectral radius is 0.9991387 estimated iterations to convergence 269 setup time was (sec) 1.840000 now iterating at: 18:23:53 rms-change max change #iterations 9.059574 339.6418 at 10iterations 5.060032 114.4183 at 20iterations 2.809375 61.45587 at 30iterations 1.560202 33.81062 at 40iterations 0.8610182 18.00712 at 50iterations 0.4770295 9.394890 at 60iterations 0.2626483 5.224498 at 70iterations 0.1448523 2.925097 at 80iterations 7.9690449E-02 1.541916 at 90iterations 4.3984495E-02 0.9095640 at 100iterations 2.4141263E-02 0.5173130 at 110iterations 1.3336412E-02 0.2664127 at 120iterations 7.3222448E-03 0.1506689 at 130iterations 4.0302118E-03 8.6363316E-02 at 140iterations 2.2193044E-03 4.7912598E-02 at 150iterations 1.2224172E-03 2.3814052E-02 at 160iterations 6.7736296E-04 1.4026165E-02 at 170iterations 3.7559151E-04 8.1534386E-03 at 180iterations finished qdiffx linear iterations at : 18:24:07 total time elapsed so far: 15.55000 # loops : 180 mean,max change (kT/e) : 3.7559151E-04 8.1534386E-03 energy calculations done at 15.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.74000 DelPhi exited at 18:24:07 15.737u 0.316s 0:16.33 98.2% 0+0k 0+0io 0pf+0w