Mon Oct 10 14:04:23 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 Mon Oct 10 2011 at 14:04:24 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3284 !!! WARNING: SEP 61 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5952480 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): -1.668000 58.13900 ymin,ymax (A): -24.84800 27.13900 zmin,zma (A): -9.697001 45.56600 x,y,z range (A): 59.80700 51.98700 55.26300 scale (grids/A): 0.5952480 object centre (A): 28.23550 1.145500 17.93450 number of atom coordinates read : 3284 total number of charged atoms : 3135 net assigned charge : 2.025009 assigned positive charge : 491.6668 centred at (gu) : 91.61761 89.13560 90.27648 assigned negative charge : -489.6432 centred at (gu) : 91.67911 89.15578 90.25293 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7601 nv = 96 ne = 84 npr = 67945 no. pairs analyzed = 67945 no. exposed pairs = 3847 no. arc points = 26614 no. surface atoms = 1298 nbur = 1986 mkacc time = 0.1400000 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 = 1.456000 m= 347 mr = 4281 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.3600000 number of dielectric boundary points 3640 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2644 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9589 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4778172E-10 1.8131524E-09 midg,1,midg; midg,igrid,midg 1.9121988E-09 -1.4883324E-11 1,midg,midg; igrid,midg,midg 2.2049853E-09 -2.4727769E-09 gauss-seidel spectral radius is 0.9854470 estimated iterations to convergence 68 setup time was (sec) 0.6100000 now iterating at: 14:04:24 rms-change max change #iterations 0.1183670 16.18424 at 10iterations 9.9558448E-03 1.718884 at 20iterations 8.4475148E-04 0.1319523 at 30iterations 8.2169841E-05 1.1707306E-02 at 40iterations 1.1214070E-05 1.6582012E-03 at 50iterations finished qdiffx linear iterations at : 14:04:27 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.1214070E-05 1.6582012E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 14:04:28 3.439u 0.197s 0:04.06 89.1% 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 Mon Oct 10 2011 at 14:04:28 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3284 !!! WARNING: SEP 61 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.785744 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): -1.668000 58.13900 ymin,ymax (A): -24.84800 27.13900 zmin,zma (A): -9.697001 45.56600 x,y,z range (A): 59.80700 51.98700 55.26300 scale (grids/A): 1.785744 object centre (A): 28.23550 1.145500 17.93450 number of atom coordinates read : 3284 total number of charged atoms : 3135 net assigned charge : 2.025009 assigned positive charge : 491.6668 centred at (gu) : 94.85213 87.40572 90.82855 assigned negative charge : -489.6432 centred at (gu) : 95.03695 87.46711 90.75872 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 83676 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26614 grid for indexing accessible points = 1.400000 m= 28332 mr = 59366 m= 3536 mr = 20530 m= 128 mr = 2023 m= 0 mr = 27 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2197 time to turn everything in is 0.5900000 number of dielectric boundary points 33726 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 221 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 24406 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) : 0.5952480 object centre at (A) : 28.23550 1.145500 17.93450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.9432991E-03 -2.3374261E-02 midg,1,midg; midg,igrid,midg 9.1615114E-03 7.6362081E-03 1,midg,midg; igrid,midg,midg 2.5071373E-02 8.5324254E-03 gauss-seidel spectral radius is 0.9985156 estimated iterations to convergence 206 setup time was (sec) 0.8900000 now iterating at: 14:04:29 rms-change max change #iterations 4.268481 200.8959 at 10iterations 1.932590 61.35872 at 20iterations 0.8735219 28.31644 at 30iterations 0.3968350 12.19268 at 40iterations 0.1797518 5.773721 at 50iterations 8.1893899E-02 2.490446 at 60iterations 3.7124608E-02 1.176539 at 70iterations 1.6856017E-02 0.5306454 at 80iterations 7.6874504E-03 0.2534943 at 90iterations 3.4804379E-03 0.1048641 at 100iterations 1.5868362E-03 4.7274590E-02 at 110iterations 7.2134996E-04 2.3138046E-02 at 120iterations finished qdiffx linear iterations at : 14:04:36 total time elapsed so far: 8.420000 # loops : 120 mean,max change (kT/e) : 7.2134996E-04 2.3138046E-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) 8.590000 DelPhi exited at 14:04:37 8.590u 0.227s 0:09.56 92.1% 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 Mon Oct 10 2011 at 14:04:37 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3284 !!! WARNING: SEP 61 has a net charge of -0.4750 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: 2.678616 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): -1.668000 58.13900 ymin,ymax (A): -24.84800 27.13900 zmin,zma (A): -9.697001 45.56600 x,y,z range (A): 59.80700 51.98700 55.26300 scale (grids/A): 2.678616 object centre (A): 28.23550 1.145500 17.93450 number of atom coordinates read : 3284 total number of charged atoms : 3135 net assigned charge : 2.025009 assigned positive charge : 491.6668 centred at (gu) : 97.27798 86.10848 91.24268 assigned negative charge : -489.6432 centred at (gu) : 97.55540 86.20050 91.13786 start vw surface at 0.1600000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 194072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26614 grid for indexing accessible points = 1.400000 m= 95244 mr = 144012 m= 30481 mr = 77682 m= 5867 mr = 23959 m= 520 mr = 4145 m= 19 mr = 319 m= 0 mr = 6 time to grow re-entrant surface = 0.8100000 no. cavity mid-points inaccessible to solvent = 7414 time to turn everything in is 1.420000 number of dielectric boundary points 76080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.560000 number of grid points assigned charge 25071 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) : 1.785744 object centre at (A) : 28.23550 1.145500 17.93450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6317274E-02 -0.3408235 midg,1,midg; midg,igrid,midg 3.9521057E-02 0.1009588 1,midg,midg; igrid,midg,midg 0.3058697 0.1980364 gauss-seidel spectral radius is 0.9992383 estimated iterations to convergence 286 setup time was (sec) 1.740000 now iterating at: 14:04:39 rms-change max change #iterations 10.27495 293.7068 at 10iterations 5.962763 139.9195 at 20iterations 3.429060 67.79742 at 30iterations 1.975125 36.19584 at 40iterations 1.130507 22.77240 at 50iterations 0.6457318 12.25450 at 60iterations 0.3694706 6.558352 at 70iterations 0.2108767 3.806891 at 80iterations 0.1202868 2.095341 at 90iterations 6.8538859E-02 1.247530 at 100iterations 3.9112147E-02 0.6706753 at 110iterations 2.2328177E-02 0.3962193 at 120iterations 1.2735315E-02 0.2192688 at 130iterations 7.2572245E-03 0.1315556 at 140iterations 4.1299625E-03 7.1987152E-02 at 150iterations 2.3633670E-03 4.1535378E-02 at 160iterations 1.3477318E-03 2.3590565E-02 at 170iterations 7.7093666E-04 1.4992237E-02 at 180iterations finished qdiffx linear iterations at : 14:04:51 total time elapsed so far: 13.77000 # loops : 180 mean,max change (kT/e) : 7.7093666E-04 1.4992237E-02 energy calculations done at 13.77000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.94000 DelPhi exited at 14:04:52 13.942u 0.237s 0:14.54 97.4% 0+0k 0+0io 0pf+0w