Mon Oct 10 19:33:57 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 19:33:57 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 = 2405 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: 0.6838526 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): -16.68000 35.37800 ymin,ymax (A): -7.218000 37.77600 zmin,zma (A): -2.227000 49.28500 x,y,z range (A): 52.05800 44.99400 51.51200 scale (grids/A): 0.6838526 object centre (A): 9.349001 15.27900 23.52900 number of atom coordinates read : 2405 total number of charged atoms : 2269 net assigned charge : 2.000004 assigned positive charge : 358.8559 centred at (gu) : 92.32613 90.49709 90.89582 assigned negative charge : -356.8565 centred at (gu) : 92.23812 90.66295 90.96267 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7686 nv = 96 ne = 84 npr = 48816 no. pairs analyzed = 48816 no. exposed pairs = 3164 no. arc points = 21623 no. surface atoms = 1063 nbur = 1342 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 506 mr = 4204 m= 2 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 17 time to turn everything in is 0.2100000 number of dielectric boundary points 3903 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1963 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8731 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5810548E-08 -1.5383504E-08 midg,1,midg; midg,igrid,midg 5.6418958E-08 -5.0746998E-08 1,midg,midg; igrid,midg,midg -1.2117610E-08 6.0829059E-08 gauss-seidel spectral radius is 0.9888987 estimated iterations to convergence 77 setup time was (sec) 0.4000000 now iterating at: 19:33:57 rms-change max change #iterations 0.1822886 28.11419 at 10iterations 2.0994890E-02 2.544426 at 20iterations 2.5210348E-03 0.4065094 at 30iterations 3.6294566E-04 5.1221848E-02 at 40iterations 8.6606786E-05 1.3768196E-02 at 50iterations finished qdiffx linear iterations at : 19:34:00 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 8.6606786E-05 1.3768196E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 19:34:01 3.418u 0.164s 0:03.90 91.5% 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 19:34:01 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 = 2405 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: 2.051558 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): -16.68000 35.37800 ymin,ymax (A): -7.218000 37.77600 zmin,zma (A): -2.227000 49.28500 x,y,z range (A): 52.05800 44.99400 51.51200 scale (grids/A): 2.051558 object centre (A): 9.349001 15.27900 23.52900 number of atom coordinates read : 2405 total number of charged atoms : 2269 net assigned charge : 2.000004 assigned positive charge : 358.8559 centred at (gu) : 96.97773 91.49077 92.68698 assigned negative charge : -356.8565 centred at (gu) : 96.71436 91.98848 92.88774 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81546 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21623 grid for indexing accessible points = 1.400000 m= 32139 mr = 56442 m= 6548 mr = 23856 m= 671 mr = 4317 m= 17 mr = 347 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 868 time to turn everything in is 0.4300000 number of dielectric boundary points 35959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17991 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) : 0.6838526 object centre at (A) : 9.349001 15.27900 23.52900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4817044E-02 1.2983692E-02 midg,1,midg; midg,igrid,midg 2.7612109E-02 -1.2914452E-03 1,midg,midg; igrid,midg,midg -7.3031285E-03 2.1853581E-02 gauss-seidel spectral radius is 0.9987976 estimated iterations to convergence 228 setup time was (sec) 0.6500000 now iterating at: 19:34:02 rms-change max change #iterations 4.691561 295.6635 at 10iterations 2.290104 72.41159 at 20iterations 1.128681 34.84415 at 30iterations 0.5519171 16.34280 at 40iterations 0.2709189 7.782652 at 50iterations 0.1331349 4.192965 at 60iterations 6.5401480E-02 2.039227 at 70iterations 3.2125074E-02 0.9353638 at 80iterations 1.5744889E-02 0.4485197 at 90iterations 7.7552721E-03 0.2185955 at 100iterations 3.8375105E-03 0.1186681 at 110iterations 1.9051298E-03 5.2660942E-02 at 120iterations finished qdiffx linear iterations at : 19:34:09 total time elapsed so far: 7.800000 # loops : 120 mean,max change (kT/e) : 1.9051298E-03 5.2660942E-02 energy calculations done at 7.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 19:34:09 7.933u 0.204s 0:08.53 95.3% 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 Mon Oct 10 2011 at 19:34:09 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 = 2405 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: 3.077337 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): -16.68000 35.37800 ymin,ymax (A): -7.218000 37.77600 zmin,zma (A): -2.227000 49.28500 x,y,z range (A): 52.05800 44.99400 51.51200 scale (grids/A): 3.077337 object centre (A): 9.349001 15.27900 23.52900 number of atom coordinates read : 2405 total number of charged atoms : 2269 net assigned charge : 2.000004 assigned positive charge : 358.8559 centred at (gu) : 100.4665 92.23602 94.03040 assigned negative charge : -356.8565 centred at (gu) : 100.0714 92.98280 94.33150 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 188129 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21623 grid for indexing accessible points = 1.400000 m= 99294 mr = 136546 m= 41210 mr = 81311 m= 12515 mr = 33540 m= 2715 mr = 9624 m= 305 mr = 2019 m= 9 mr = 200 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 2703 time to turn everything in is 1.290000 number of dielectric boundary points 80937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 18151 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) : 2.051558 object centre at (A) : 9.349001 15.27900 23.52900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4030972 0.6393064 midg,1,midg; midg,igrid,midg 0.2052671 0.1788009 1,midg,midg; igrid,midg,midg 2.1489324E-02 5.2904621E-02 gauss-seidel spectral radius is 0.9993007 estimated iterations to convergence 298 setup time was (sec) 1.520000 now iterating at: 19:34:11 rms-change max change #iterations 10.75942 542.5279 at 10iterations 6.402231 155.7817 at 20iterations 3.794474 89.60814 at 30iterations 2.251172 39.76608 at 40iterations 1.328205 25.84122 at 50iterations 0.7812051 13.88677 at 60iterations 0.4598051 8.281482 at 70iterations 0.2691627 4.574737 at 80iterations 0.1579610 2.806322 at 90iterations 9.2573136E-02 1.685524 at 100iterations 5.4406174E-02 0.9627609 at 110iterations 3.1727120E-02 0.6233120 at 120iterations 1.8589024E-02 0.3005581 at 130iterations 1.0891641E-02 0.1913137 at 140iterations 6.3757454E-03 0.1034412 at 150iterations 3.7508612E-03 6.1323166E-02 at 160iterations 2.2193205E-03 3.5610199E-02 at 170iterations 1.3268838E-03 2.6950836E-02 at 180iterations finished qdiffx linear iterations at : 19:34:23 total time elapsed so far: 13.03000 # loops : 180 mean,max change (kT/e) : 1.3268838E-03 2.6950836E-02 energy calculations done at 13.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.17000 DelPhi exited at 19:34:24 13.175u 0.221s 0:14.16 94.5% 0+0k 0+0io 0pf+0w