Mon Oct 10 14:15:35 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 14:15:35 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2941 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: 0.5867616 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): -30.06500 30.60700 ymin,ymax (A): 12.46100 71.52700 zmin,zma (A): -36.40200 19.06700 x,y,z range (A): 60.67200 59.06600 55.46899 scale (grids/A): 0.5867616 object centre (A): 0.2709999 41.99400 -8.667499 number of atom coordinates read : 2941 total number of charged atoms : 2750 net assigned charge : 9.500025 assigned positive charge : 448.7751 centred at (gu) : 90.49180 90.65728 90.87297 assigned negative charge : -439.2761 centred at (gu) : 90.42577 90.67302 90.80058 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6735 nv = 96 ne = 84 npr = 57632 no. pairs analyzed = 57632 no. exposed pairs = 3897 no. arc points = 27787 no. surface atoms = 1303 nbur = 1638 mkacc time = 0.1500000 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 = 1.456000 m= 358 mr = 3453 m= 0 mr = 22 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3618 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2788 ## 326 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8428 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.1973315E-10 5.5504459E-09 midg,1,midg; midg,igrid,midg 2.6034559E-09 2.5049529E-09 1,midg,midg; igrid,midg,midg 7.1407807E-10 4.8917013E-09 gauss-seidel spectral radius is 0.9850077 estimated iterations to convergence 67 setup time was (sec) 0.6400000 now iterating at: 14:15:36 rms-change max change #iterations 0.1077264 16.03754 at 10iterations 8.6517176E-03 1.358453 at 20iterations 7.2556786E-04 9.4654083E-02 at 30iterations 9.5937496E-05 1.6048431E-02 at 40iterations 2.5786629E-05 4.7106743E-03 at 50iterations finished qdiffx linear iterations at : 14:15:41 total time elapsed so far: 5.160000 # loops : 50 mean,max change (kT/e) : 2.5786629E-05 4.7106743E-03 energy calculations done at 5.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.310000 DelPhi exited at 14:15:42 5.319u 0.439s 0:06.11 93.9% 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 14:15:42 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2941 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: 1.760285 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): -30.06500 30.60700 ymin,ymax (A): 12.46100 71.52700 zmin,zma (A): -36.40200 19.06700 x,y,z range (A): 60.67200 59.06600 55.46899 scale (grids/A): 1.760285 object centre (A): 0.2709999 41.99400 -8.667499 number of atom coordinates read : 2941 total number of charged atoms : 2750 net assigned charge : 9.500025 assigned positive charge : 448.7751 centred at (gu) : 91.47469 91.97116 92.61827 assigned negative charge : -439.2761 centred at (gu) : 91.27718 92.01866 92.40124 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 73568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27787 grid for indexing accessible points = 1.400000 m= 23470 mr = 49090 m= 3148 mr = 16076 m= 121 mr = 1682 m= 4 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 169 time to turn everything in is 0.6200000 number of dielectric boundary points 33446 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 244 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 21283 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) : 0.5867616 object centre at (A) : 0.2709999 41.99400 -8.667499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4688461E-03 2.0978965E-02 midg,1,midg; midg,igrid,midg 1.3641239E-02 1.8406570E-02 1,midg,midg; igrid,midg,midg -1.2311365E-02 1.8888187E-02 gauss-seidel spectral radius is 0.9984427 estimated iterations to convergence 201 setup time was (sec) 1.000000 now iterating at: 14:15:43 rms-change max change #iterations 3.953721 179.8538 at 10iterations 1.748947 63.04107 at 20iterations 0.7777881 25.08832 at 30iterations 0.3453456 12.01703 at 40iterations 0.1528039 4.774097 at 50iterations 6.7939721E-02 2.178579 at 60iterations 3.0273631E-02 0.9581451 at 70iterations 1.3462774E-02 0.4928896 at 80iterations 5.9927297E-03 0.2052355 at 90iterations 2.6737766E-03 8.9851379E-02 at 100iterations 1.1880965E-03 3.9081573E-02 at 110iterations 5.2902271E-04 1.7522454E-02 at 120iterations finished qdiffx linear iterations at : 14:15:54 total time elapsed so far: 12.13000 # loops : 120 mean,max change (kT/e) : 5.2902271E-04 1.7522454E-02 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 14:15:55 12.300u 0.502s 0:13.44 95.2% 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 14:15:55 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: 340 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2941 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: 2.640427 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): -30.06500 30.60700 ymin,ymax (A): 12.46100 71.52700 zmin,zma (A): -36.40200 19.06700 x,y,z range (A): 60.67200 59.06600 55.46899 scale (grids/A): 2.640427 object centre (A): 0.2709999 41.99400 -8.667499 number of atom coordinates read : 2941 total number of charged atoms : 2750 net assigned charge : 9.500025 assigned positive charge : 448.7751 centred at (gu) : 92.21186 92.95661 93.92721 assigned negative charge : -439.2761 centred at (gu) : 91.91549 93.02805 93.60183 start vw surface at 0.1200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 170519 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27787 grid for indexing accessible points = 1.400000 m= 79266 mr = 120111 m= 25015 mr = 62382 m= 5222 mr = 18743 m= 529 mr = 3557 m= 19 mr = 272 m= 0 mr = 2 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 630 time to turn everything in is 1.570000 number of dielectric boundary points 75503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 21987 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) : 1.760285 object centre at (A) : 0.2709999 41.99400 -8.667499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.2359612E-03 0.1804702 midg,1,midg; midg,igrid,midg 0.1751309 0.2723378 1,midg,midg; igrid,midg,midg -0.1346702 4.4084843E-02 gauss-seidel spectral radius is 0.9992149 estimated iterations to convergence 282 setup time was (sec) 1.940000 now iterating at: 14:15:58 rms-change max change #iterations 9.825473 377.4232 at 10iterations 5.733479 144.2701 at 20iterations 3.315541 77.46204 at 30iterations 1.901771 41.45492 at 40iterations 1.089502 21.66652 at 50iterations 0.6201670 12.00807 at 60iterations 0.3540158 7.662810 at 70iterations 0.2013854 3.993977 at 80iterations 0.1143223 2.355437 at 90iterations 6.4908050E-02 1.294671 at 100iterations 3.6701757E-02 0.7821436 at 110iterations 2.0800514E-02 0.3956165 at 120iterations 1.1816220E-02 0.2267003 at 130iterations 6.6796225E-03 0.1324005 at 140iterations 3.7840626E-03 7.4920654E-02 at 150iterations 2.1494890E-03 4.6335220E-02 at 160iterations 1.2203294E-03 2.3988247E-02 at 170iterations 6.9874118E-04 1.4200211E-02 at 180iterations finished qdiffx linear iterations at : 14:16:17 total time elapsed so far: 21.40000 # loops : 180 mean,max change (kT/e) : 6.9874118E-04 1.4200211E-02 energy calculations done at 21.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.56000 DelPhi exited at 14:16:18 21.565u 0.537s 0:22.63 97.6% 0+0k 0+0io 0pf+0w