Tue Oct 11 06:57:07 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 Tue Oct 11 2011 at 06:57:07 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 0.5448090 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): -20.70400 44.64000 ymin,ymax (A): 21.75800 77.83500 zmin,zma (A): -71.08801 -22.81600 x,y,z range (A): 65.34400 56.07700 48.27200 scale (grids/A): 0.5448090 object centre (A): 11.96800 49.79650 -46.95200 number of atom coordinates read : 2976 total number of charged atoms : 2833 net assigned charge : -2.460989 assigned positive charge : 435.5186 centred at (gu) : 89.69679 89.91501 89.58636 assigned negative charge : -437.9802 centred at (gu) : 89.66872 90.01817 89.55774 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 5690 nv = 96 ne = 84 npr = 62084 no. pairs analyzed = 62084 no. exposed pairs = 3642 no. arc points = 25628 no. surface atoms = 1235 nbur = 1741 mkacc time = 0.1700000 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 = 1.568000 m= 216 mr = 3018 m= 0 mr = 14 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 2874 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2581 ## 324 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7469 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6044648E-10 2.9654775E-11 midg,1,midg; midg,igrid,midg 5.0412746E-10 -7.8369955E-10 1,midg,midg; igrid,midg,midg -3.4696651E-10 2.7502348E-11 gauss-seidel spectral radius is 0.9826310 estimated iterations to convergence 63 setup time was (sec) 0.6500000 now iterating at: 06:57:08 rms-change max change #iterations 7.3055796E-02 11.95018 at 10iterations 5.0506536E-03 0.7770472 at 20iterations 3.5713171E-04 5.7060242E-02 at 30iterations 3.8095572E-05 8.5396767E-03 at 40iterations 6.4714668E-06 1.6002655E-03 at 50iterations finished qdiffx linear iterations at : 06:57:11 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 6.4714668E-06 1.6002655E-03 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.120000 DelPhi exited at 06:57:12 4.126u 0.264s 0:04.93 88.8% 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 Tue Oct 11 2011 at 06:57:12 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 1.634427 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): -20.70400 44.64000 ymin,ymax (A): 21.75800 77.83500 zmin,zma (A): -71.08801 -22.81600 x,y,z range (A): 65.34400 56.07700 48.27200 scale (grids/A): 1.634427 object centre (A): 11.96800 49.79650 -46.95200 number of atom coordinates read : 2976 total number of charged atoms : 2833 net assigned charge : -2.460989 assigned positive charge : 435.5186 centred at (gu) : 89.08958 89.74438 88.75850 assigned negative charge : -437.9802 centred at (gu) : 89.00587 90.05434 88.67291 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 63005 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25628 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19704 mr = 42917 m= 2113 mr = 13975 m= 39 mr = 1114 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 224 time to turn everything in is 0.5600000 number of dielectric boundary points 26849 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 254 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 21703 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) : 0.5448090 object centre at (A) : 11.96800 49.79650 -46.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5505678E-03 8.2270494E-03 midg,1,midg; midg,igrid,midg -3.6420340E-03 3.3935136E-03 1,midg,midg; igrid,midg,midg -1.0329746E-02 -2.0773958E-02 gauss-seidel spectral radius is 0.9981892 estimated iterations to convergence 187 setup time was (sec) 0.8600000 now iterating at: 06:57:13 rms-change max change #iterations 3.297163 147.7388 at 10iterations 1.376650 54.65164 at 20iterations 0.5741431 21.99044 at 30iterations 0.2407173 9.128910 at 40iterations 0.1005751 4.026488 at 50iterations 4.2016562E-02 1.557150 at 60iterations 1.7535387E-02 0.5865765 at 70iterations 7.3288116E-03 0.2614608 at 80iterations 3.0599982E-03 0.1141281 at 90iterations 1.2826531E-03 5.5683613E-02 at 100iterations 5.3579680E-04 2.3029327E-02 at 110iterations 2.2409453E-04 7.9040527E-03 at 120iterations finished qdiffx linear iterations at : 06:57:22 total time elapsed so far: 9.010000 # loops : 120 mean,max change (kT/e) : 2.2409453E-04 7.9040527E-03 energy calculations done at 9.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.180000 DelPhi exited at 06:57:22 9.182u 0.322s 0:09.92 95.7% 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 Tue Oct 11 2011 at 06:57:22 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2976 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 has a net charge of 0.5140 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: 2.451640 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): -20.70400 44.64000 ymin,ymax (A): 21.75800 77.83500 zmin,zma (A): -71.08801 -22.81600 x,y,z range (A): 65.34400 56.07700 48.27200 scale (grids/A): 2.451640 object centre (A): 11.96800 49.79650 -46.95200 number of atom coordinates read : 2976 total number of charged atoms : 2833 net assigned charge : -2.460989 assigned positive charge : 435.5186 centred at (gu) : 88.63424 89.61638 88.13766 assigned negative charge : -437.9802 centred at (gu) : 88.50882 90.08128 88.00945 start vw surface at 0.1700000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 146447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25628 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 68036 mr = 105079 m= 19859 mr = 54421 m= 3184 mr = 15407 m= 234 mr = 2193 m= 7 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 887 time to turn everything in is 1.400000 number of dielectric boundary points 60536 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 22636 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) : 1.634427 object centre at (A) : 11.96800 49.79650 -46.95200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.1814935E-02 0.1382328 midg,1,midg; midg,igrid,midg -4.0717892E-02 6.5488763E-02 1,midg,midg; igrid,midg,midg -0.1775464 -0.4459637 gauss-seidel spectral radius is 0.9991380 estimated iterations to convergence 269 setup time was (sec) 1.730000 now iterating at: 06:57:24 rms-change max change #iterations 8.512215 311.2661 at 10iterations 4.753983 133.5624 at 20iterations 2.649040 61.91322 at 30iterations 1.467455 32.94181 at 40iterations 0.8138469 17.56933 at 50iterations 0.4494396 9.869342 at 60iterations 0.2478489 5.440334 at 70iterations 0.1365556 2.996975 at 80iterations 7.5273842E-02 1.565075 at 90iterations 4.1332994E-02 0.8200502 at 100iterations 2.2684764E-02 0.4563646 at 110iterations 1.2480796E-02 0.2791481 at 120iterations 6.8635992E-03 0.1426487 at 130iterations 3.7695954E-03 7.5954437E-02 at 140iterations 2.0657261E-03 4.3901443E-02 at 150iterations 1.1374085E-03 2.4617910E-02 at 160iterations 6.2548730E-04 1.3332367E-02 at 170iterations 3.4418734E-04 6.5078735E-03 at 180iterations finished qdiffx linear iterations at : 06:57:37 total time elapsed so far: 14.96000 # loops : 180 mean,max change (kT/e) : 3.4418734E-04 6.5078735E-03 energy calculations done at 14.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.13000 DelPhi exited at 06:57:38 15.136u 0.283s 0:15.79 97.5% 0+0k 0+0io 0pf+0w