Tue Oct 11 08:06:55 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 08:06:55 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 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: 0.5412144 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): -20.43000 43.21400 ymin,ymax (A): -2.101000 63.67700 zmin,zma (A): 3.344000 54.88500 x,y,z range (A): 63.64400 65.77800 51.54100 scale (grids/A): 0.5412144 object centre (A): 11.39200 30.78800 29.11450 number of atom coordinates read : 3122 total number of charged atoms : 2976 net assigned charge : 11.50002 assigned positive charge : 466.8107 centred at (gu) : 89.71903 90.57128 90.71328 assigned negative charge : -455.3120 centred at (gu) : 89.57890 90.60989 90.76353 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6200 nv = 96 ne = 84 npr = 57970 no. pairs analyzed = 57970 no. exposed pairs = 4406 no. arc points = 31984 no. surface atoms = 1478 nbur = 1644 mkacc time = 0.1600000 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= 242 mr = 2887 m= 0 mr = 6 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3176 ## 434 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7960 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.4200773E-10 3.6885736E-10 midg,1,midg; midg,igrid,midg 7.1158995E-10 4.3420970E-10 1,midg,midg; igrid,midg,midg -2.2863997E-10 1.2891771E-09 gauss-seidel spectral radius is 0.9824336 estimated iterations to convergence 62 setup time was (sec) 0.6600000 now iterating at: 08:06:56 rms-change max change #iterations 7.1699776E-02 11.33611 at 10iterations 4.5854631E-03 0.7513447 at 20iterations 2.9967283E-04 5.3552628E-02 at 30iterations 2.0697276E-05 3.1166077E-03 at 40iterations 1.7606847E-06 2.3651123E-04 at 50iterations finished qdiffx linear iterations at : 08:06:59 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 1.7606847E-06 2.3651123E-04 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 08:07:00 4.204u 0.269s 0:04.97 89.7% 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 08:07:00 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 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: 1.623643 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): -20.43000 43.21400 ymin,ymax (A): -2.101000 63.67700 zmin,zma (A): 3.344000 54.88500 x,y,z range (A): 63.64400 65.77800 51.54100 scale (grids/A): 1.623643 object centre (A): 11.39200 30.78800 29.11450 number of atom coordinates read : 3122 total number of charged atoms : 2976 net assigned charge : 11.50002 assigned positive charge : 466.8107 centred at (gu) : 89.15613 91.71277 92.13876 assigned negative charge : -455.3120 centred at (gu) : 88.73622 91.82948 92.29028 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 68288 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31984 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19314 mr = 43043 m= 1836 mr = 12519 m= 54 mr = 764 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 573 time to turn everything in is 0.6100000 number of dielectric boundary points 33166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 428 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22807 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) : 0.5412144 object centre at (A) : 11.39200 30.78800 29.11450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8277624E-03 1.0822972E-02 midg,1,midg; midg,igrid,midg -6.3690683E-03 -9.9820811E-03 1,midg,midg; igrid,midg,midg 2.0978998E-03 2.5610311E-02 gauss-seidel spectral radius is 0.9981996 estimated iterations to convergence 187 setup time was (sec) 0.9000000 now iterating at: 08:07:01 rms-change max change #iterations 3.340313 153.2226 at 10iterations 1.387839 56.47919 at 20iterations 0.5766641 22.32771 at 30iterations 0.2405775 8.907990 at 40iterations 0.1001521 3.946411 at 50iterations 4.1649982E-02 1.638383 at 60iterations 1.7385252E-02 0.6911087 at 70iterations 7.2740898E-03 0.2729740 at 80iterations 3.0336410E-03 0.1060677 at 90iterations 1.2624222E-03 4.7173023E-02 at 100iterations 5.2881124E-04 1.9172668E-02 at 110iterations 2.2108051E-04 8.1844330E-03 at 120iterations finished qdiffx linear iterations at : 08:07:09 total time elapsed so far: 9.350000 # loops : 120 mean,max change (kT/e) : 2.2108051E-04 8.1844330E-03 energy calculations done at 9.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 08:07:10 9.538u 0.318s 0:10.43 94.3% 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 Tue Oct 11 2011 at 08:07:10 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3122 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: 2.435465 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): -20.43000 43.21400 ymin,ymax (A): -2.101000 63.67700 zmin,zma (A): 3.344000 54.88500 x,y,z range (A): 63.64400 65.77800 51.54100 scale (grids/A): 2.435465 object centre (A): 11.39200 30.78800 29.11450 number of atom coordinates read : 3122 total number of charged atoms : 2976 net assigned charge : 11.50002 assigned positive charge : 466.8107 centred at (gu) : 88.73392 92.56895 93.20787 assigned negative charge : -455.3120 centred at (gu) : 88.10431 92.74398 93.43538 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 158507 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31984 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67557 mr = 106389 m= 17942 mr = 51415 m= 2625 mr = 12714 m= 175 mr = 1532 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.8600001 no. cavity mid-points inaccessible to solvent = 1824 time to turn everything in is 1.470000 number of dielectric boundary points 74689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.610000 number of grid points assigned charge 23779 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) : 1.623643 object centre at (A) : 11.39200 30.78800 29.11450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.2302272E-02 0.1664416 midg,1,midg; midg,igrid,midg -0.1183634 -0.1034366 1,midg,midg; igrid,midg,midg 7.1537741E-02 0.3356722 gauss-seidel spectral radius is 0.9991548 estimated iterations to convergence 272 setup time was (sec) 1.790000 now iterating at: 08:07:12 rms-change max change #iterations 8.795338 274.7736 at 10iterations 5.026226 141.5850 at 20iterations 2.844349 69.17448 at 30iterations 1.600828 40.08189 at 40iterations 0.8982776 22.10180 at 50iterations 0.4987776 11.15094 at 60iterations 0.2779531 6.325397 at 70iterations 0.1540752 3.603683 at 80iterations 8.5587502E-02 1.774916 at 90iterations 4.7443867E-02 0.9989147 at 100iterations 2.6283372E-02 0.5400238 at 110iterations 1.4506888E-02 0.3184795 at 120iterations 8.0165174E-03 0.1547346 at 130iterations 4.4260635E-03 9.9643707E-02 at 140iterations 2.4468149E-03 4.9560547E-02 at 150iterations 1.3497480E-03 2.5998116E-02 at 160iterations 7.4628240E-04 1.4644623E-02 at 170iterations 4.1262011E-04 8.2244873E-03 at 180iterations finished qdiffx linear iterations at : 08:07:26 total time elapsed so far: 15.72000 # loops : 180 mean,max change (kT/e) : 4.1262011E-04 8.2244873E-03 energy calculations done at 15.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.90000 DelPhi exited at 08:07:27 15.906u 0.332s 0:16.81 96.5% 0+0k 0+0io 0pf+0w