Sat Oct 15 13:19:39 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 Sat Oct 15 2011 at 13:19:40 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 = 2576 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: 0.6296873 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): -12.36600 37.15300 ymin,ymax (A): -22.25000 34.28600 zmin,zma (A): -12.19900 40.80300 x,y,z range (A): 49.51900 56.53600 53.00200 scale (grids/A): 0.6296873 object centre (A): 12.39350 6.018000 14.30200 number of atom coordinates read : 2576 total number of charged atoms : 2432 net assigned charge : 5.000012 assigned positive charge : 389.0199 centred at (gu) : 90.75522 89.40200 90.17709 assigned negative charge : -384.0206 centred at (gu) : 90.71671 89.37217 90.17480 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6624 nv = 96 ne = 84 npr = 52613 no. pairs analyzed = 52613 no. exposed pairs = 3094 no. arc points = 22102 no. surface atoms = 1054 nbur = 1522 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 335 mr = 3531 m= 2 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3500000 number of dielectric boundary points 3374 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2225 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 8209 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9876934E-09 5.7827561E-09 midg,1,midg; midg,igrid,midg 3.1293272E-09 7.0019843E-09 1,midg,midg; igrid,midg,midg 1.7504956E-09 1.0234259E-08 gauss-seidel spectral radius is 0.9869330 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 13:19:43 rms-change max change #iterations 0.1317540 19.13909 at 10iterations 1.2506118E-02 1.668816 at 20iterations 1.2004166E-03 0.1707115 at 30iterations 1.1323651E-04 1.8482208E-02 at 40iterations 1.1004740E-05 1.7828941E-03 at 50iterations finished qdiffx linear iterations at : 13:19:53 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 1.1004740E-05 1.7828941E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 13:19:54 4.185u 0.304s 0:14.56 30.7% 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 Sat Oct 15 2011 at 13:19:54 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 = 2576 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: 1.889062 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): -12.36600 37.15300 ymin,ymax (A): -22.25000 34.28600 zmin,zma (A): -12.19900 40.80300 x,y,z range (A): 49.51900 56.53600 53.00200 scale (grids/A): 1.889062 object centre (A): 12.39350 6.018000 14.30200 number of atom coordinates read : 2576 total number of charged atoms : 2432 net assigned charge : 5.000012 assigned positive charge : 389.0199 centred at (gu) : 92.26527 88.20553 90.53045 assigned negative charge : -384.0206 centred at (gu) : 92.14999 88.11623 90.52401 start vw surface at 0.1600000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 71980 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22102 grid for indexing accessible points = 1.400000 m= 23679 mr = 48966 m= 3691 mr = 16936 m= 229 mr = 2271 m= 0 mr = 107 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1040 time to turn everything in is 0.6500000 number of dielectric boundary points 31299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 19068 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) : 0.6296873 object centre at (A) : 12.39350 6.018000 14.30200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5300319E-03 -1.0937048E-02 midg,1,midg; midg,igrid,midg 4.3420143E-02 -9.0260792E-04 1,midg,midg; igrid,midg,midg -9.7891409E-03 5.7203337E-03 gauss-seidel spectral radius is 0.9986045 estimated iterations to convergence 212 setup time was (sec) 0.9700000 now iterating at: 13:19:57 rms-change max change #iterations 4.087219 177.1967 at 10iterations 1.893999 60.80338 at 20iterations 0.8797933 28.24631 at 30iterations 0.4083309 14.13822 at 40iterations 0.1887639 6.086423 at 50iterations 8.7765113E-02 2.942014 at 60iterations 4.0618714E-02 1.322829 at 70iterations 1.8920735E-02 0.6619692 at 80iterations 8.7602204E-03 0.2890930 at 90iterations 4.0639983E-03 0.1343040 at 100iterations 1.8879696E-03 6.2919617E-02 at 110iterations 8.7297725E-04 2.7938843E-02 at 120iterations finished qdiffx linear iterations at : 13:20:16 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 8.7297725E-04 2.7938843E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.820000 DelPhi exited at 13:20:17 9.827u 0.341s 0:22.49 45.1% 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 15 2011 at 13:20:21 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 = 2576 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: 2.833593 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): -12.36600 37.15300 ymin,ymax (A): -22.25000 34.28600 zmin,zma (A): -12.19900 40.80300 x,y,z range (A): 49.51900 56.53600 53.00200 scale (grids/A): 2.833593 object centre (A): 12.39350 6.018000 14.30200 number of atom coordinates read : 2576 total number of charged atoms : 2432 net assigned charge : 5.000012 assigned positive charge : 389.0199 centred at (gu) : 93.39793 87.30815 90.79581 assigned negative charge : -384.0206 centred at (gu) : 93.22501 87.17439 90.78600 start vw surface at 0.1700000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 166912 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22102 grid for indexing accessible points = 1.400000 m= 78702 mr = 119511 m= 26371 mr = 63314 m= 6513 mr = 20657 m= 1056 mr = 4918 m= 57 mr = 766 m= 0 mr = 35 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 3360 time to turn everything in is 1.640000 number of dielectric boundary points 70410 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 19455 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) : 1.889062 object centre at (A) : 12.39350 6.018000 14.30200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1849709 -0.3039820 midg,1,midg; midg,igrid,midg 0.4411386 0.1082665 1,midg,midg; igrid,midg,midg -0.2208907 6.8926401E-02 gauss-seidel spectral radius is 0.9992502 estimated iterations to convergence 288 setup time was (sec) 1.970000 now iterating at: 13:20:25 rms-change max change #iterations 9.715996 313.4734 at 10iterations 5.630651 120.6014 at 20iterations 3.244459 69.32893 at 30iterations 1.863179 40.09641 at 40iterations 1.066940 21.79968 at 50iterations 0.6119394 11.23849 at 60iterations 0.3499449 6.296690 at 70iterations 0.2009402 3.787409 at 80iterations 0.1148244 2.099283 at 90iterations 6.5541036E-02 1.295708 at 100iterations 3.7528608E-02 0.6831665 at 110iterations 2.1474462E-02 0.4087968 at 120iterations 1.2271582E-02 0.2299938 at 130iterations 7.0112385E-03 0.1268001 at 140iterations 4.0043821E-03 7.8531265E-02 at 150iterations 2.2895762E-03 4.1841507E-02 at 160iterations 1.3084703E-03 2.4753094E-02 at 170iterations 7.4797677E-04 1.3889313E-02 at 180iterations finished qdiffx linear iterations at : 13:20:57 total time elapsed so far: 16.39000 # loops : 180 mean,max change (kT/e) : 7.4797677E-04 1.3889313E-02 energy calculations done at 16.39000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.58000 DelPhi exited at 13:20:58 16.577u 0.375s 0:37.32 45.3% 0+0k 0+0io 0pf+0w