Mon Oct 10 14:03:39 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 14:03:39 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 0.7387578 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): -21.02900 24.51300 ymin,ymax (A): -38.44400 9.099000 zmin,zma (A): -44.68400 3.505000 x,y,z range (A): 45.54200 47.54300 48.18900 scale (grids/A): 0.7387578 object centre (A): 1.742001 -14.67250 -20.58950 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 88.85705 89.76746 89.99885 assigned negative charge : -324.1440 centred at (gu) : 88.92301 89.73903 89.79287 start vw surface at 0.1500000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8052 nv = 96 ne = 84 npr = 43771 no. pairs analyzed = 43771 no. exposed pairs = 2750 no. arc points = 19329 no. surface atoms = 932 nbur = 1196 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 546 mr = 4459 m= 2 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 38 time to turn everything in is 0.3600000 number of dielectric boundary points 4033 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1621 ## 131 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8506 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.9687195E-07 1.1618624E-07 midg,1,midg; midg,igrid,midg -1.1979505E-07 -5.5487025E-08 1,midg,midg; igrid,midg,midg -2.4131213E-08 -1.2372475E-07 gauss-seidel spectral radius is 0.9904554 estimated iterations to convergence 83 setup time was (sec) 0.6900000 now iterating at: 14:03:44 rms-change max change #iterations 0.2485566 39.91701 at 10iterations 3.4046590E-02 4.291016 at 20iterations 4.4835187E-03 0.6987839 at 30iterations 5.9832959E-04 8.3558083E-02 at 40iterations 7.9910111E-05 9.4757080E-03 at 50iterations finished qdiffx linear iterations at : 14:03:47 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 7.9910111E-05 9.4757080E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.710000 DelPhi exited at 14:03:48 4.713u 0.441s 0:08.63 59.6% 0+0k 0+0io 5pf+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 14:03:48 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 2.216274 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): -21.02900 24.51300 ymin,ymax (A): -38.44400 9.099000 zmin,zma (A): -44.68400 3.505000 x,y,z range (A): 45.54200 47.54300 48.18900 scale (grids/A): 2.216274 object centre (A): 1.742001 -14.67250 -20.58950 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 86.57102 89.30257 89.99659 assigned negative charge : -324.1440 centred at (gu) : 86.76899 89.21712 89.37862 start vw surface at 0.1500000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 84343 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19329 grid for indexing accessible points = 1.400000 m= 32877 mr = 57974 m= 6913 mr = 24622 m= 663 mr = 4737 m= 20 mr = 349 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 955 time to turn everything in is 0.9000000 number of dielectric boundary points 37134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 15848 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) : 0.7387578 object centre at (A) : 1.742001 -14.67250 -20.58950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1441716 1.7071598E-03 midg,1,midg; midg,igrid,midg -2.6592761E-02 -2.7117483E-02 1,midg,midg; igrid,midg,midg -2.2512244E-03 6.6554127E-03 gauss-seidel spectral radius is 0.9989269 estimated iterations to convergence 241 setup time was (sec) 1.260000 now iterating at: 14:04:02 rms-change max change #iterations 5.083768 220.4369 at 10iterations 2.576066 88.25417 at 20iterations 1.310764 39.11379 at 30iterations 0.6673722 19.39571 at 40iterations 0.3409069 9.957434 at 50iterations 0.1732476 4.962030 at 60iterations 8.8393360E-02 2.782745 at 70iterations 4.5076445E-02 1.375290 at 80iterations 2.2975672E-02 0.6711597 at 90iterations 1.1719677E-02 0.3131504 at 100iterations 5.9726574E-03 0.1653681 at 110iterations 3.0496104E-03 8.8401794E-02 at 120iterations finished qdiffx linear iterations at : 14:04:12 total time elapsed so far: 11.27000 # loops : 120 mean,max change (kT/e) : 3.0496104E-03 8.8401794E-02 energy calculations done at 11.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.49000 DelPhi exited at 14:04:13 11.498u 0.561s 0:24.76 48.6% 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 14:04:13 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2128 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: 3.324410 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): -21.02900 24.51300 ymin,ymax (A): -38.44400 9.099000 zmin,zma (A): -44.68400 3.505000 x,y,z range (A): 45.54200 47.54300 48.18900 scale (grids/A): 3.324410 object centre (A): 1.742001 -14.67250 -20.58950 number of atom coordinates read : 2128 total number of charged atoms : 1989 net assigned charge : -4.999980 assigned positive charge : 319.1439 centred at (gu) : 84.85647 88.95390 89.99479 assigned negative charge : -324.1440 centred at (gu) : 85.15355 88.82565 89.06791 start vw surface at 0.1300000 fill in re-entrant regions at 1.110000 boundary points on vw surface= 194230 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19329 grid for indexing accessible points = 1.400000 m= 101444 mr = 139641 m= 42271 mr = 83512 m= 13005 mr = 34568 m= 2822 mr = 10353 m= 322 mr = 2107 m= 11 mr = 182 m= 0 mr = 2 time to grow re-entrant surface = 1.460000 no. cavity mid-points inaccessible to solvent = 3070 time to turn everything in is 2.740000 number of dielectric boundary points 83740 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.910000 number of grid points assigned charge 15912 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) : 2.216274 object centre at (A) : 1.742001 -14.67250 -20.58950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.265090 0.1156178 midg,1,midg; midg,igrid,midg -0.1360531 -0.2525603 1,midg,midg; igrid,midg,midg -0.1236023 1.4244424E-02 gauss-seidel spectral radius is 0.9993198 estimated iterations to convergence 302 setup time was (sec) 3.130000 now iterating at: 14:04:16 rms-change max change #iterations 11.02292 330.9813 at 10iterations 6.494514 158.9087 at 20iterations 3.830769 70.00389 at 30iterations 2.250618 42.54893 at 40iterations 1.328185 23.03847 at 50iterations 0.7808842 13.40080 at 60iterations 0.4582427 7.560659 at 70iterations 0.2699012 4.334352 at 80iterations 0.1582970 2.818236 at 90iterations 9.2927918E-02 1.512584 at 100iterations 5.4557376E-02 0.8323627 at 110iterations 3.2067865E-02 0.5219193 at 120iterations 1.8830769E-02 0.3026047 at 130iterations 1.1053625E-02 0.1727777 at 140iterations 6.5069674E-03 9.9897385E-02 at 150iterations 3.8190244E-03 6.3171387E-02 at 160iterations 2.2410690E-03 3.5902023E-02 at 170iterations 1.3179027E-03 2.0941734E-02 at 180iterations finished qdiffx linear iterations at : 14:04:34 total time elapsed so far: 20.14000 # loops : 180 mean,max change (kT/e) : 1.3179027E-03 2.0941734E-02 energy calculations done at 20.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.35000 DelPhi exited at 14:04:34 20.354u 0.530s 0:21.49 97.1% 0+0k 0+0io 0pf+0w