Mon Oct 10 01:26:08 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 01:26:08 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 = 1964 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: 0.6452783 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): -5.340000 34.55700 ymin,ymax (A): -3.536000 49.05700 zmin,zma (A): -24.23000 30.94000 x,y,z range (A): 39.89700 52.59300 55.17000 scale (grids/A): 0.6452783 object centre (A): 14.60850 22.76050 3.355000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.64098 92.34492 90.20139 assigned negative charge : -284.8263 centred at (gu) : 90.73518 92.46644 90.13965 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5583 nv = 96 ne = 84 npr = 40213 no. pairs analyzed = 40213 no. exposed pairs = 2473 no. arc points = 17291 no. surface atoms = 843 nbur = 1121 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 280 mr = 3140 m= 2 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1686 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6532 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.2661409E-10 1.1935010E-08 midg,1,midg; midg,igrid,midg 1.0498240E-08 -1.1371093E-08 1,midg,midg; igrid,midg,midg 1.2716933E-08 -4.5305040E-09 gauss-seidel spectral radius is 0.9874993 estimated iterations to convergence 73 setup time was (sec) 0.5300000 now iterating at: 01:26:09 rms-change max change #iterations 0.1266807 21.00102 at 10iterations 1.2744366E-02 2.191333 at 20iterations 1.2944058E-03 0.1977386 at 30iterations 1.2734429E-04 1.7033577E-02 at 40iterations 1.2803516E-05 2.4986267E-03 at 50iterations finished qdiffx linear iterations at : 01:26:12 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 1.2803516E-05 2.4986267E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 01:26:12 3.593u 0.232s 0:04.25 89.8% 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 Mon Oct 10 2011 at 01:26:12 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 = 1964 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: 1.935835 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): -5.340000 34.55700 ymin,ymax (A): -3.536000 49.05700 zmin,zma (A): -24.23000 30.94000 x,y,z range (A): 39.89700 52.59300 55.17000 scale (grids/A): 1.935835 object centre (A): 14.60850 22.76050 3.355000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 91.92305 97.03458 90.60429 assigned negative charge : -284.8263 centred at (gu) : 92.20558 97.39956 90.41914 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 59861 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17291 grid for indexing accessible points = 1.400000 m= 21885 mr = 41278 m= 3229 mr = 16623 m= 134 mr = 2106 m= 1 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 679 time to turn everything in is 0.5000000 number of dielectric boundary points 25065 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 14448 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) : 0.6452783 object centre at (A) : 14.60850 22.76050 3.355000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1097251E-02 1.6953593E-02 midg,1,midg; midg,igrid,midg 3.4196414E-02 -8.6404560E-03 1,midg,midg; igrid,midg,midg 4.5326045E-03 -4.6773162E-03 gauss-seidel spectral radius is 0.9985995 estimated iterations to convergence 212 setup time was (sec) 0.8100000 now iterating at: 01:26:13 rms-change max change #iterations 3.659058 204.0685 at 10iterations 1.696813 67.91112 at 20iterations 0.7871469 30.76902 at 30iterations 0.3675109 14.89087 at 40iterations 0.1690421 5.821095 at 50iterations 7.8332074E-02 2.675877 at 60iterations 3.6302108E-02 1.214943 at 70iterations 1.6849678E-02 0.6095777 at 80iterations 7.8151934E-03 0.2592201 at 90iterations 3.6210266E-03 0.1300240 at 100iterations 1.6814403E-03 6.6999435E-02 at 110iterations 7.8026974E-04 3.1082153E-02 at 120iterations finished qdiffx linear iterations at : 01:26:21 total time elapsed so far: 7.910000 # loops : 120 mean,max change (kT/e) : 7.8026974E-04 3.1082153E-02 energy calculations done at 7.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 01:26:21 8.101u 0.253s 0:08.71 95.8% 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 Mon Oct 10 2011 at 01:26:21 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 = 1964 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: 2.903752 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): -5.340000 34.55700 ymin,ymax (A): -3.536000 49.05700 zmin,zma (A): -24.23000 30.94000 x,y,z range (A): 39.89700 52.59300 55.17000 scale (grids/A): 2.903752 object centre (A): 14.60850 22.76050 3.355000 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 92.88462 100.5519 90.90643 assigned negative charge : -284.8263 centred at (gu) : 93.30840 101.0993 90.62871 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 138126 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17291 grid for indexing accessible points = 1.400000 m= 70391 mr = 99583 m= 25949 mr = 58538 m= 5889 mr = 21522 m= 650 mr = 4530 m= 27 mr = 422 m= 0 mr = 5 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 2281 time to turn everything in is 1.190000 number of dielectric boundary points 56432 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 14656 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) : 1.935835 object centre at (A) : 14.60850 22.76050 3.355000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.145741 6.3533209E-02 midg,1,midg; midg,igrid,midg 0.3606621 -0.1241977 1,midg,midg; igrid,midg,midg 2.1283051E-02 -2.7850175E-02 gauss-seidel spectral radius is 0.9992351 estimated iterations to convergence 285 setup time was (sec) 1.520000 now iterating at: 01:26:23 rms-change max change #iterations 8.601393 514.5587 at 10iterations 4.960773 124.6950 at 20iterations 2.828329 82.25153 at 30iterations 1.616273 52.09871 at 40iterations 0.9223226 25.44250 at 50iterations 0.5251871 14.03080 at 60iterations 0.3000668 6.305065 at 70iterations 0.1705327 3.508488 at 80iterations 9.7201727E-02 1.953566 at 90iterations 5.5158321E-02 1.066187 at 100iterations 3.1436943E-02 0.5743542 at 110iterations 1.7860303E-02 0.4608078 at 120iterations 1.0129799E-02 0.1965714 at 130iterations 5.7669566E-03 0.1261444 at 140iterations 3.2714109E-03 6.2072754E-02 at 150iterations 1.8616788E-03 3.6249161E-02 at 160iterations 1.0572543E-03 2.2186279E-02 at 170iterations 6.0152839E-04 1.1749268E-02 at 180iterations finished qdiffx linear iterations at : 01:26:34 total time elapsed so far: 12.70000 # loops : 180 mean,max change (kT/e) : 6.0152839E-04 1.1749268E-02 energy calculations done at 12.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 01:26:35 12.894u 0.276s 0:13.54 97.1% 0+0k 0+0io 0pf+0w