Mon Oct 10 14:07:19 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 14:07:19 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 = 3020 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5768639 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): -6.123000 55.59000 ymin,ymax (A): -14.74600 46.27700 zmin,zma (A): -20.09100 36.73400 x,y,z range (A): 61.71300 61.02300 56.82500 scale (grids/A): 0.5768639 object centre (A): 24.73350 15.76550 8.321501 number of atom coordinates read : 3020 total number of charged atoms : 2881 net assigned charge : -4.499986 assigned positive charge : 443.0212 centred at (gu) : 92.34470 91.14748 89.73425 assigned negative charge : -447.5219 centred at (gu) : 92.42111 91.11554 89.75475 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6930 nv = 96 ne = 84 npr = 57144 no. pairs analyzed = 57144 no. exposed pairs = 4286 no. arc points = 31307 no. surface atoms = 1408 nbur = 1612 mkacc time = 9.9999994E-02 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 = 1.484000 m= 338 mr = 3331 m= 2 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2200000 number of dielectric boundary points 3918 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3021 ## 350 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 8614 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.6391971E-10 -1.1754396E-09 midg,1,midg; midg,igrid,midg -1.1334137E-09 -2.6563801E-10 1,midg,midg; igrid,midg,midg 3.6341660E-10 -4.1471071E-09 gauss-seidel spectral radius is 0.9845153 estimated iterations to convergence 66 setup time was (sec) 0.4200000 now iterating at: 14:07:20 rms-change max change #iterations 9.9115171E-02 17.04164 at 10iterations 7.4667740E-03 1.154977 at 20iterations 5.7572423E-04 8.4003448E-02 at 30iterations 4.4082870E-05 6.5956116E-03 at 40iterations 3.9780484E-06 6.5165758E-04 at 50iterations finished qdiffx linear iterations at : 14:07:23 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 3.9780484E-06 6.5165758E-04 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 14:07:23 3.570u 0.455s 0:04.45 90.3% 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 14:07:23 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 = 3020 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.730592 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): -6.123000 55.59000 ymin,ymax (A): -14.74600 46.27700 zmin,zma (A): -20.09100 36.73400 x,y,z range (A): 61.71300 61.02300 56.82500 scale (grids/A): 1.730592 object centre (A): 24.73350 15.76550 8.321501 number of atom coordinates read : 3020 total number of charged atoms : 2881 net assigned charge : -4.499986 assigned positive charge : 443.0212 centred at (gu) : 97.03326 93.44173 89.20187 assigned negative charge : -447.5219 centred at (gu) : 97.26261 93.34619 89.26389 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 76123 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31307 grid for indexing accessible points = 1.400000 m= 22965 mr = 49103 m= 2679 mr = 15040 m= 122 mr = 1161 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 2599 time to turn everything in is 0.3600000 number of dielectric boundary points 36562 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 278 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 22345 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) : 0.5768639 object centre at (A) : 24.73350 15.76550 8.321501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6624042E-03 1.0629397E-02 midg,1,midg; midg,igrid,midg -7.0805899E-03 -1.2878701E-02 1,midg,midg; igrid,midg,midg 9.1246731E-04 -2.2432707E-02 gauss-seidel spectral radius is 0.9984275 estimated iterations to convergence 200 setup time was (sec) 0.5900000 now iterating at: 14:07:24 rms-change max change #iterations 3.779230 177.9010 at 10iterations 1.662144 60.37901 at 20iterations 0.7331786 25.32870 at 30iterations 0.3238590 12.80482 at 40iterations 0.1427182 4.632483 at 50iterations 6.3140444E-02 2.000592 at 60iterations 2.7917504E-02 0.9073448 at 70iterations 1.2361700E-02 0.4122009 at 80iterations 5.4522031E-03 0.2072353 at 90iterations 2.4163544E-03 8.6678505E-02 at 100iterations 1.0680658E-03 3.7464142E-02 at 110iterations 4.7227481E-04 1.4869690E-02 at 120iterations finished qdiffx linear iterations at : 14:07:32 total time elapsed so far: 8.420000 # loops : 120 mean,max change (kT/e) : 4.7227481E-04 1.4869690E-02 energy calculations done at 8.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.570000 DelPhi exited at 14:07:33 8.570u 0.235s 0:09.99 88.0% 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 14:07:34 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 = 3020 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: 2.595887 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): -6.123000 55.59000 ymin,ymax (A): -14.74600 46.27700 zmin,zma (A): -20.09100 36.73400 x,y,z range (A): 61.71300 61.02300 56.82500 scale (grids/A): 2.595887 object centre (A): 24.73350 15.76550 8.321501 number of atom coordinates read : 3020 total number of charged atoms : 2881 net assigned charge : -4.499986 assigned positive charge : 443.0212 centred at (gu) : 100.5498 95.16224 88.80251 assigned negative charge : -447.5219 centred at (gu) : 100.8937 95.01903 88.89573 start vw surface at 0.1200000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 176362 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31307 grid for indexing accessible points = 1.400000 m= 78550 mr = 120707 m= 22956 mr = 60045 m= 4115 mr = 16622 m= 437 mr = 2537 m= 12 mr = 216 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 8860 time to turn everything in is 0.9300000 number of dielectric boundary points 82305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 23042 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) : 1.730592 object centre at (A) : 24.73350 15.76550 8.321501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8627578E-02 0.1483110 midg,1,midg; midg,igrid,midg -4.3571532E-02 -0.1568619 1,midg,midg; igrid,midg,midg 1.4780890E-02 -0.1032961 gauss-seidel spectral radius is 0.9992350 estimated iterations to convergence 285 setup time was (sec) 1.180000 now iterating at: 14:07:35 rms-change max change #iterations 9.608407 266.7526 at 10iterations 5.661931 133.7857 at 20iterations 3.291368 70.50658 at 30iterations 1.910306 44.26553 at 40iterations 1.100650 22.57232 at 50iterations 0.6340255 13.25616 at 60iterations 0.3633510 7.246332 at 70iterations 0.2077518 4.593624 at 80iterations 0.1189420 2.339966 at 90iterations 6.7830808E-02 1.454538 at 100iterations 3.8635783E-02 0.7311454 at 110iterations 2.2012474E-02 0.4937554 at 120iterations 1.2566673E-02 0.2244505 at 130iterations 7.1484540E-03 0.1367188 at 140iterations 4.0646461E-03 7.8528762E-02 at 150iterations 2.3195220E-03 4.8815727E-02 at 160iterations 1.3193499E-03 2.6021957E-02 at 170iterations 7.5041159E-04 1.5346527E-02 at 180iterations finished qdiffx linear iterations at : 14:07:47 total time elapsed so far: 12.67000 # loops : 180 mean,max change (kT/e) : 7.5041159E-04 1.5346527E-02 energy calculations done at 12.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 14:07:47 12.808u 0.241s 0:13.60 95.8% 0+0k 0+0io 0pf+0w