Sat Oct 8 15:57:50 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 Sat Oct 8 2011 at 15:57:51 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 = 2314 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6474493 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): -1.571000 47.69000 ymin,ymax (A): -16.00500 30.01100 zmin,zma (A): -18.64200 36.34300 x,y,z range (A): 49.26100 46.01600 54.98500 scale (grids/A): 0.6474493 object centre (A): 23.05950 7.003000 8.850499 number of atom coordinates read : 2314 total number of charged atoms : 2210 net assigned charge : 5.000005 assigned positive charge : 339.1862 centred at (gu) : 89.92009 88.64554 90.25317 assigned negative charge : -334.1869 centred at (gu) : 89.98190 88.77796 90.26758 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6460 nv = 96 ne = 84 npr = 47434 no. pairs analyzed = 47434 no. exposed pairs = 2884 no. arc points = 19932 no. surface atoms = 991 nbur = 1323 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 382 mr = 3567 m= 0 mr = 50 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3225 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1983 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7836 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.9752295E-09 7.3382034E-09 midg,1,midg; midg,igrid,midg 3.3049613E-08 -5.6712204E-09 1,midg,midg; igrid,midg,midg 1.6547608E-08 1.1029379E-09 gauss-seidel spectral radius is 0.9876133 estimated iterations to convergence 73 setup time was (sec) 0.5900000 now iterating at: 15:57:51 rms-change max change #iterations 0.1418753 23.78259 at 10iterations 1.4645689E-02 2.197427 at 20iterations 1.5103655E-03 0.2414093 at 30iterations 1.7131290E-04 2.4673462E-02 at 40iterations 2.4688063E-05 4.1351318E-03 at 50iterations finished qdiffx linear iterations at : 15:57:55 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 2.4688063E-05 4.1351318E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 15:57:55 4.057u 0.284s 0:04.82 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 Sat Oct 8 2011 at 15:57:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2314 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.942348 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): -1.571000 47.69000 ymin,ymax (A): -16.00500 30.01100 zmin,zma (A): -18.64200 36.34300 x,y,z range (A): 49.26100 46.01600 54.98500 scale (grids/A): 1.942348 object centre (A): 23.05950 7.003000 8.850499 number of atom coordinates read : 2314 total number of charged atoms : 2210 net assigned charge : 5.000005 assigned positive charge : 339.1862 centred at (gu) : 89.75938 85.93607 90.75903 assigned negative charge : -334.1869 centred at (gu) : 89.94561 86.33377 90.80249 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 69723 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19932 grid for indexing accessible points = 1.400000 m= 25172 mr = 48401 m= 4533 mr = 18443 m= 341 mr = 3022 m= 9 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 29777 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 121 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17444 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) : 0.6474493 object centre at (A) : 23.05950 7.003000 8.850499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6956666E-02 6.7799399E-03 midg,1,midg; midg,igrid,midg 2.6946977E-02 -3.1547109E-03 1,midg,midg; igrid,midg,midg 9.3406504E-03 -3.0081186E-02 gauss-seidel spectral radius is 0.9986571 estimated iterations to convergence 216 setup time was (sec) 0.9200000 now iterating at: 15:57:57 rms-change max change #iterations 4.065975 169.9067 at 10iterations 1.905521 72.34988 at 20iterations 0.8952853 27.95989 at 30iterations 0.4228333 14.01805 at 40iterations 0.1989640 6.925798 at 50iterations 9.3832955E-02 3.209308 at 60iterations 4.4208623E-02 1.494659 at 70iterations 2.0832155E-02 0.6964998 at 80iterations 9.8220501E-03 0.3209076 at 90iterations 4.6533314E-03 0.1551585 at 100iterations 2.1947632E-03 7.4743748E-02 at 110iterations 1.0392716E-03 3.2817841E-02 at 120iterations finished qdiffx linear iterations at : 15:58:05 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 1.0392716E-03 3.2817841E-02 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.330000 DelPhi exited at 15:58:05 9.335u 0.298s 0:09.90 97.1% 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 Sat Oct 8 2011 at 15:58:05 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 = 2314 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.913522 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): -1.571000 47.69000 ymin,ymax (A): -16.00500 30.01100 zmin,zma (A): -18.64200 36.34300 x,y,z range (A): 49.26100 46.01600 54.98500 scale (grids/A): 2.913522 object centre (A): 23.05950 7.003000 8.850499 number of atom coordinates read : 2314 total number of charged atoms : 2210 net assigned charge : 5.000005 assigned positive charge : 339.1862 centred at (gu) : 89.63894 83.90395 91.13848 assigned negative charge : -334.1869 centred at (gu) : 89.91850 84.50076 91.20368 start vw surface at 0.1300000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 161358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19932 grid for indexing accessible points = 1.400000 m= 80390 mr = 117254 m= 30383 mr = 65461 m= 8416 mr = 24539 m= 1407 mr = 6590 m= 129 mr = 973 m= 4 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 67193 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 17679 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) : 1.942348 object centre at (A) : 23.05950 7.003000 8.850499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.6533336E-02 -1.1999333E-02 midg,1,midg; midg,igrid,midg 0.2152407 -5.6511223E-02 1,midg,midg; igrid,midg,midg 6.8934366E-02 -0.4036940 gauss-seidel spectral radius is 0.9992589 estimated iterations to convergence 290 setup time was (sec) 1.920000 now iterating at: 15:58:08 rms-change max change #iterations 9.531153 433.4237 at 10iterations 5.612049 155.5889 at 20iterations 3.259612 79.85176 at 30iterations 1.904273 36.44578 at 40iterations 1.107639 21.15227 at 50iterations 0.6405917 13.19616 at 60iterations 0.3705921 7.477242 at 70iterations 0.2139412 4.254715 at 80iterations 0.1234428 2.633657 at 90iterations 7.1196564E-02 1.470364 at 100iterations 4.0928632E-02 0.7604275 at 110iterations 2.3671892E-02 0.4446182 at 120iterations 1.3589036E-02 0.2768764 at 130iterations 7.8247944E-03 0.1428604 at 140iterations 4.5108930E-03 8.0610275E-02 at 150iterations 2.5947934E-03 4.8388481E-02 at 160iterations 1.4963243E-03 2.6396751E-02 at 170iterations 8.6707529E-04 1.6677856E-02 at 180iterations finished qdiffx linear iterations at : 15:58:21 total time elapsed so far: 15.61000 # loops : 180 mean,max change (kT/e) : 8.6707529E-04 1.6677856E-02 energy calculations done at 15.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.78000 DelPhi exited at 15:58:22 15.786u 0.328s 0:16.39 98.2% 0+0k 0+0io 0pf+0w