Tue Oct 11 06:54:58 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 Tue Oct 11 2011 at 06:54:58 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 = 2965 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: 0.5653127 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): -18.35100 44.62300 ymin,ymax (A): 19.41100 77.06400 zmin,zma (A): -69.85400 -19.09300 x,y,z range (A): 62.97400 57.65300 50.76100 scale (grids/A): 0.5653127 object centre (A): 13.13600 48.23750 -44.47350 number of atom coordinates read : 2965 total number of charged atoms : 2825 net assigned charge : -1.999990 assigned positive charge : 432.4116 centred at (gu) : 89.61961 89.61572 89.38824 assigned negative charge : -434.4122 centred at (gu) : 89.60629 89.72395 89.36151 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6259 nv = 96 ne = 84 npr = 60879 no. pairs analyzed = 60879 no. exposed pairs = 3676 no. arc points = 26256 no. surface atoms = 1248 nbur = 1717 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 = 1.512000 m= 276 mr = 3279 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3237 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2708 ## 316 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8057 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0762818E-10 7.3325908E-11 midg,1,midg; midg,igrid,midg 1.2467817E-09 -1.5427075E-09 1,midg,midg; igrid,midg,midg -4.7627929E-10 -8.0574790E-11 gauss-seidel spectral radius is 0.9838601 estimated iterations to convergence 65 setup time was (sec) 0.6100000 now iterating at: 06:54:59 rms-change max change #iterations 8.4606014E-02 13.36577 at 10iterations 6.2032710E-03 1.064257 at 20iterations 4.6701889E-04 8.7918282E-02 at 30iterations 4.2254207E-05 8.2893372E-03 at 40iterations 5.7337866E-06 1.3866425E-03 at 50iterations finished qdiffx linear iterations at : 06:55:02 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 5.7337866E-06 1.3866425E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 06:55:02 3.390u 0.219s 0:03.93 91.6% 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 Tue Oct 11 2011 at 06:55:02 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 = 2965 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: 1.695938 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): -18.35100 44.62300 ymin,ymax (A): 19.41100 77.06400 zmin,zma (A): -69.85400 -19.09300 x,y,z range (A): 62.97400 57.65300 50.76100 scale (grids/A): 1.695938 object centre (A): 13.13600 48.23750 -44.47350 number of atom coordinates read : 2965 total number of charged atoms : 2825 net assigned charge : -1.999990 assigned positive charge : 432.4116 centred at (gu) : 88.85819 88.84660 88.16424 assigned negative charge : -434.4122 centred at (gu) : 88.81875 89.17181 88.08413 start vw surface at 0.1700000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 68499 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26256 grid for indexing accessible points = 1.400000 m= 23222 mr = 46602 m= 2868 mr = 16680 m= 83 mr = 1567 m= 0 mr = 16 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5000000 number of dielectric boundary points 29807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 245 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 21856 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) : 0.5653127 object centre at (A) : 13.13600 48.23750 -44.47350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7951724E-03 1.2849592E-02 midg,1,midg; midg,igrid,midg -2.3337784E-03 3.9602607E-03 1,midg,midg; igrid,midg,midg -8.2420195E-03 -3.2575373E-02 gauss-seidel spectral radius is 0.9983284 estimated iterations to convergence 194 setup time was (sec) 0.7700000 now iterating at: 06:55:03 rms-change max change #iterations 3.573393 155.5796 at 10iterations 1.535912 54.56155 at 20iterations 0.6633161 24.49684 at 30iterations 0.2872467 9.936665 at 40iterations 0.1241356 4.493359 at 50iterations 5.3554539E-02 1.912548 at 60iterations 2.3172667E-02 0.8159204 at 70iterations 9.9834530E-03 0.3229971 at 80iterations 4.3303547E-03 0.1526031 at 90iterations 1.8650847E-03 6.8188190E-02 at 100iterations 8.0870616E-04 2.6590347E-02 at 110iterations 3.4872256E-04 1.1929512E-02 at 120iterations finished qdiffx linear iterations at : 06:55:09 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 3.4872256E-04 1.1929512E-02 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 06:55:10 7.101u 0.172s 0:07.58 95.9% 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 Tue Oct 11 2011 at 06:55:10 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 = 2965 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: 2.543907 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): -18.35100 44.62300 ymin,ymax (A): 19.41100 77.06400 zmin,zma (A): -69.85400 -19.09300 x,y,z range (A): 62.97400 57.65300 50.76100 scale (grids/A): 2.543907 object centre (A): 13.13600 48.23750 -44.47350 number of atom coordinates read : 2965 total number of charged atoms : 2825 net assigned charge : -1.999990 assigned positive charge : 432.4116 centred at (gu) : 88.28718 88.26968 87.24608 assigned negative charge : -434.4122 centred at (gu) : 88.22792 88.75757 87.12599 start vw surface at 0.1500000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 158752 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26256 grid for indexing accessible points = 1.400000 m= 77043 mr = 113446 m= 24975 mr = 62109 m= 4787 mr = 19530 m= 411 mr = 3467 m= 14 mr = 198 m= 0 mr = 5 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 67227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 22580 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) : 1.695938 object centre at (A) : 13.13600 48.23750 -44.47350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1080883 0.2755068 midg,1,midg; midg,igrid,midg -7.2356880E-02 7.7111751E-02 1,midg,midg; igrid,midg,midg -0.1548842 -0.4087167 gauss-seidel spectral radius is 0.9991849 estimated iterations to convergence 277 setup time was (sec) 1.510000 now iterating at: 06:55:12 rms-change max change #iterations 8.935170 262.9888 at 10iterations 5.094290 135.2436 at 20iterations 2.885985 62.76532 at 30iterations 1.630804 32.44485 at 40iterations 0.9159531 18.09731 at 50iterations 0.5156374 11.14765 at 60iterations 0.2898322 5.727366 at 70iterations 0.1624139 3.297659 at 80iterations 9.0769820E-02 1.767929 at 90iterations 5.0863307E-02 0.9532623 at 100iterations 2.8439729E-02 0.5735359 at 110iterations 1.5896788E-02 0.3398092 at 120iterations 8.8738957E-03 0.1780357 at 130iterations 4.9660183E-03 9.7326279E-02 at 140iterations 2.7757534E-03 5.5469513E-02 at 150iterations 1.5497890E-03 2.9624939E-02 at 160iterations 8.6666958E-04 1.5918732E-02 at 170iterations 4.8423238E-04 1.1131287E-02 at 180iterations finished qdiffx linear iterations at : 06:55:22 total time elapsed so far: 11.79000 # loops : 180 mean,max change (kT/e) : 4.8423238E-04 1.1131287E-02 energy calculations done at 11.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.96000 DelPhi exited at 06:55:22 11.967u 0.254s 0:12.52 97.5% 0+0k 0+0io 0pf+0w