Wed Feb 15 08:55:41 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:42 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 = 2741 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: 0.5643090 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): -36.13100 18.25400 ymin,ymax (A): -13.96800 29.96500 zmin,zma (A): 10.83600 73.92200 x,y,z range (A): 54.38500 43.93300 63.08601 scale (grids/A): 0.5643090 object centre (A): -8.938500 7.998500 42.37900 number of atom coordinates read : 2741 total number of charged atoms : 2601 net assigned charge : 1.000028 assigned positive charge : 405.6168 centred at (gu) : 91.12924 90.33399 90.16993 assigned negative charge : -404.6176 centred at (gu) : 91.12644 90.24017 90.15861 start vw surface at 0.1800000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5598 nv = 96 ne = 84 npr = 56660 no. pairs analyzed = 56660 no. exposed pairs = 3464 no. arc points = 25072 no. surface atoms = 1174 nbur = 1567 mkacc time = 0.1400000 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 = 1.512000 m= 241 mr = 2854 m= 0 mr = 12 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3400000 number of dielectric boundary points 2973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2560 ## 319 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7351 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1960970E-11 2.6341249E-10 midg,1,midg; midg,igrid,midg -9.1482949E-10 1.3107797E-09 1,midg,midg; igrid,midg,midg 6.7708124E-11 1.9999577E-10 gauss-seidel spectral radius is 0.9837812 estimated iterations to convergence 65 setup time was (sec) 0.5900000 now iterating at: 08:55:43 rms-change max change #iterations 7.9877198E-02 14.71938 at 10iterations 5.9583797E-03 1.054644 at 20iterations 4.2889782E-04 6.8095207E-02 at 30iterations 3.7316557E-05 7.8439713E-03 at 40iterations 5.0695949E-06 1.3065338E-03 at 50iterations finished qdiffx linear iterations at : 08:55:45 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 5.0695949E-06 1.3065338E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 08:55:46 3.467u 0.174s 0:04.65 78.0% 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 Wed Feb 15 2012 at 08:55:46 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 = 2741 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.692927 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): -36.13100 18.25400 ymin,ymax (A): -13.96800 29.96500 zmin,zma (A): 10.83600 73.92200 x,y,z range (A): 54.38500 43.93300 63.08601 scale (grids/A): 1.692927 object centre (A): -8.938500 7.998500 42.37900 number of atom coordinates read : 2741 total number of charged atoms : 2601 net assigned charge : 1.000028 assigned positive charge : 405.6168 centred at (gu) : 93.38737 91.00155 90.50958 assigned negative charge : -404.6176 centred at (gu) : 93.37908 90.72041 90.47563 start vw surface at 0.2200000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 61622 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25072 grid for indexing accessible points = 1.400000 m= 18995 mr = 40924 m= 2116 mr = 13238 m= 45 mr = 1077 m= 0 mr = 8 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1602 time to turn everything in is 0.5900000 number of dielectric boundary points 27531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 244 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 20073 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) : 0.5643090 object centre at (A) : -8.938500 7.998500 42.37900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3591498E-02 4.3338970E-03 midg,1,midg; midg,igrid,midg -2.4315869E-03 5.8372347E-03 1,midg,midg; igrid,midg,midg 4.4515221E-03 -2.1455206E-03 gauss-seidel spectral radius is 0.9982929 estimated iterations to convergence 192 setup time was (sec) 0.9200000 now iterating at: 08:55:48 rms-change max change #iterations 3.401013 157.8334 at 10iterations 1.450323 57.10306 at 20iterations 0.6174665 24.18055 at 30iterations 0.2650203 9.400393 at 40iterations 0.1134574 4.244726 at 50iterations 4.8488013E-02 1.705856 at 60iterations 2.0725651E-02 0.7628294 at 70iterations 8.8658892E-03 0.3480492 at 80iterations 3.8056357E-03 0.1327324 at 90iterations 1.6292403E-03 6.3838959E-02 at 100iterations 6.9994194E-04 2.8135300E-02 at 110iterations 3.0074443E-04 1.0595083E-02 at 120iterations finished qdiffx linear iterations at : 08:55:55 total time elapsed so far: 8.240000 # loops : 120 mean,max change (kT/e) : 3.0074443E-04 1.0595083E-02 energy calculations done at 8.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.430000 DelPhi exited at 08:55:56 8.430u 0.363s 0:09.83 89.4% 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 Wed Feb 15 2012 at 08:55:56 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 = 2741 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: 2.539390 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): -36.13100 18.25400 ymin,ymax (A): -13.96800 29.96500 zmin,zma (A): 10.83600 73.92200 x,y,z range (A): 54.38500 43.93300 63.08601 scale (grids/A): 2.539390 object centre (A): -8.938500 7.998500 42.37900 number of atom coordinates read : 2741 total number of charged atoms : 2601 net assigned charge : 1.000028 assigned positive charge : 405.6168 centred at (gu) : 95.08084 91.50212 90.76426 assigned negative charge : -404.6176 centred at (gu) : 95.06865 91.08052 90.71330 start vw surface at 0.1800000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 143036 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25072 grid for indexing accessible points = 1.400000 m= 64967 mr = 100519 m= 19397 mr = 51278 m= 3328 mr = 14726 m= 277 mr = 2279 m= 5 mr = 146 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 5389 time to turn everything in is 1.190000 number of dielectric boundary points 62062 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 20798 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) : 1.692927 object centre at (A) : -8.938500 7.998500 42.37900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2407009 4.1098934E-02 midg,1,midg; midg,igrid,midg -3.1849761E-02 5.2506018E-02 1,midg,midg; igrid,midg,midg 4.7268707E-02 0.1182831 gauss-seidel spectral radius is 0.9991696 estimated iterations to convergence 274 setup time was (sec) 1.530000 now iterating at: 08:55:58 rms-change max change #iterations 8.593657 294.1144 at 10iterations 4.870429 121.9025 at 20iterations 2.737854 68.38057 at 30iterations 1.531573 36.62123 at 40iterations 0.8578849 18.98287 at 50iterations 0.4788136 10.42005 at 60iterations 0.2669247 6.065705 at 70iterations 0.1484608 2.908817 at 80iterations 8.2556486E-02 1.718945 at 90iterations 4.6061583E-02 1.017035 at 100iterations 2.5572354E-02 0.5575485 at 110iterations 1.4197233E-02 0.2897816 at 120iterations 7.9064136E-03 0.1608553 at 130iterations 4.3754452E-03 0.1033535 at 140iterations 2.4371606E-03 4.9066067E-02 at 150iterations 1.3566551E-03 3.0379772E-02 at 160iterations 7.5533451E-04 1.5740871E-02 at 170iterations 4.2154631E-04 9.9043846E-03 at 180iterations finished qdiffx linear iterations at : 08:56:10 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 4.2154631E-04 9.9043846E-03 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 08:56:11 13.336u 0.279s 0:14.51 93.7% 0+0k 0+0io 0pf+0w