Mon Oct 10 16:21:25 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 Mon Oct 10 2011 at 16:21:25 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4641 !!! WARNING: GLM 131 has a net charge of -0.0940 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: 0.5514848 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): -63.08400 -7.478000 ymin,ymax (A): -34.76000 29.79300 zmin,zma (A): -29.23600 33.33700 x,y,z range (A): 55.60600 64.55300 62.57300 scale (grids/A): 0.5514848 object centre (A): -35.28100 -2.483501 2.050499 number of atom coordinates read : 4641 total number of charged atoms : 4479 net assigned charge : 5.906019 assigned positive charge : 697.6582 centred at (gu) : 90.36066 90.17891 88.73648 assigned negative charge : -691.7562 centred at (gu) : 90.37354 90.21164 88.74992 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 9099 nv = 96 ne = 84 npr = 94780 no. pairs analyzed = 94780 no. exposed pairs = 5682 no. arc points = 38638 no. surface atoms = 1924 nbur = 2717 mkacc time = 0.1600000 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 = 1.540000 m= 365 mr = 4959 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 4485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3918 ## 475 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 12048 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4720447E-10 2.1178961E-10 midg,1,midg; midg,igrid,midg 8.2924373E-10 3.8019084E-11 1,midg,midg; igrid,midg,midg 5.6501126E-10 3.1535130E-10 gauss-seidel spectral radius is 0.9831668 estimated iterations to convergence 63 setup time was (sec) 0.5300000 now iterating at: 16:21:25 rms-change max change #iterations 9.8395750E-02 15.12636 at 10iterations 7.4904221E-03 1.147202 at 20iterations 1.3421470E-03 0.2344570 at 30iterations 5.4478121E-04 8.3919525E-02 at 40iterations 2.4550818E-04 3.2508850E-02 at 50iterations finished qdiffx linear iterations at : 16:21:28 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 2.4550818E-04 3.2508850E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 16:21:29 3.561u 0.148s 0:03.99 92.7% 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 16:21:29 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4641 !!! WARNING: GLM 131 has a net charge of -0.0940 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: 1.654454 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): -63.08400 -7.478000 ymin,ymax (A): -34.76000 29.79300 zmin,zma (A): -29.23600 33.33700 x,y,z range (A): 55.60600 64.55300 62.57300 scale (grids/A): 1.654454 object centre (A): -35.28100 -2.483501 2.050499 number of atom coordinates read : 4641 total number of charged atoms : 4479 net assigned charge : 5.906019 assigned positive charge : 697.6582 centred at (gu) : 91.08054 90.53548 86.20794 assigned negative charge : -691.7562 centred at (gu) : 91.12027 90.63455 86.24886 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 102333 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38638 grid for indexing accessible points = 1.400000 m= 33103 mr = 72709 m= 3642 mr = 23154 m= 118 mr = 1859 m= 0 mr = 25 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 608 time to turn everything in is 0.4900000 number of dielectric boundary points 41449 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 433 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 34448 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) : 0.5514848 object centre at (A) : -35.28100 -2.483501 2.050499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4023775E-02 -5.5109872E-03 midg,1,midg; midg,igrid,midg 6.0914131E-03 1.4844324E-02 1,midg,midg; igrid,midg,midg 6.6804034E-03 2.6615446E-03 gauss-seidel spectral radius is 0.9983983 estimated iterations to convergence 198 setup time was (sec) 0.7000000 now iterating at: 16:21:30 rms-change max change #iterations 4.399368 181.1145 at 10iterations 1.935266 63.71370 at 20iterations 0.8510447 24.51123 at 30iterations 0.3745223 10.48221 at 40iterations 0.1650999 4.676020 at 50iterations 7.2689325E-02 2.250436 at 60iterations 3.2242298E-02 0.9020443 at 70iterations 1.4297857E-02 0.4372401 at 80iterations 6.4702635E-03 0.1966963 at 90iterations 3.0615709E-03 9.0339661E-02 at 100iterations 1.5600426E-03 4.7250748E-02 at 110iterations 9.1027317E-04 2.6756287E-02 at 120iterations finished qdiffx linear iterations at : 16:21:37 total time elapsed so far: 7.930000 # loops : 120 mean,max change (kT/e) : 9.1027317E-04 2.6756287E-02 energy calculations done at 7.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.070000 DelPhi exited at 16:21:37 8.072u 0.198s 0:08.57 96.3% 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 16:21:37 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4641 !!! WARNING: GLM 131 has a net charge of -0.0940 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: 2.481682 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): -63.08400 -7.478000 ymin,ymax (A): -34.76000 29.79300 zmin,zma (A): -29.23600 33.33700 x,y,z range (A): 55.60600 64.55300 62.57300 scale (grids/A): 2.481682 object centre (A): -35.28100 -2.483501 2.050499 number of atom coordinates read : 4641 total number of charged atoms : 4479 net assigned charge : 5.906019 assigned positive charge : 697.6582 centred at (gu) : 91.62057 90.80294 84.31136 assigned negative charge : -691.7562 centred at (gu) : 91.68038 90.95170 84.37304 start vw surface at 0.1300000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 238171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38638 grid for indexing accessible points = 1.400000 m= 114361 mr = 177825 m= 33570 mr = 91560 m= 5779 mr = 25378 m= 501 mr = 3890 m= 21 mr = 247 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 2247 time to turn everything in is 1.240000 number of dielectric boundary points 93503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 35788 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) : 1.654454 object centre at (A) : -35.28100 -2.483501 2.050499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3383023 -0.1459190 midg,1,midg; midg,igrid,midg 2.5930248E-02 0.3265989 1,midg,midg; igrid,midg,midg 0.1178271 3.9687257E-02 gauss-seidel spectral radius is 0.9992403 estimated iterations to convergence 286 setup time was (sec) 1.490000 now iterating at: 16:21:39 rms-change max change #iterations 11.42467 289.2749 at 10iterations 6.775182 140.8706 at 20iterations 3.968865 91.34865 at 30iterations 2.322487 52.61164 at 40iterations 1.352529 29.77358 at 50iterations 0.7848011 15.65456 at 60iterations 0.4534735 7.789459 at 70iterations 0.2622734 4.499363 at 80iterations 0.1509648 3.115278 at 90iterations 8.6895585E-02 1.449463 at 100iterations 4.9986437E-02 0.8619285 at 110iterations 2.8687511E-02 0.4894753 at 120iterations 1.6502917E-02 0.2870483 at 130iterations 9.4838552E-03 0.1634593 at 140iterations 5.4710074E-03 9.0635300E-02 at 150iterations 3.1846289E-03 5.9316158E-02 at 160iterations 1.8804608E-03 3.0107498E-02 at 170iterations 1.1447789E-03 1.9189835E-02 at 180iterations finished qdiffx linear iterations at : 16:21:51 total time elapsed so far: 13.29000 # loops : 180 mean,max change (kT/e) : 1.1447789E-03 1.9189835E-02 energy calculations done at 13.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.42000 DelPhi exited at 16:21:51 13.420u 0.189s 0:13.90 97.8% 0+0k 0+0io 0pf+0w