Tue Oct 11 08:33:18 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 08:33:18 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: SEP 177 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7334157 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): 41.26300 88.46301 ymin,ymax (A): -28.90400 13.25400 zmin,zma (A): -3.033000 45.50700 x,y,z range (A): 47.20001 42.15800 48.54000 scale (grids/A): 0.7334157 object centre (A): 64.86300 -7.825000 21.23700 number of atom coordinates read : 2120 total number of charged atoms : 1988 net assigned charge : 5.564012 assigned positive charge : 325.3420 centred at (gu) : 89.13541 89.69302 90.54100 assigned negative charge : -319.7781 centred at (gu) : 89.26738 89.60467 90.46274 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7868 nv = 96 ne = 84 npr = 42527 no. pairs analyzed = 42527 no. exposed pairs = 2457 no. arc points = 16867 no. surface atoms = 841 nbur = 1279 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 545 mr = 4735 m= 4 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.1700000 number of dielectric boundary points 3568 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1417 ## 119 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8280 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2981521E-08 1.6884009E-07 midg,1,midg; midg,igrid,midg 4.7369926E-09 1.5235230E-07 1,midg,midg; igrid,midg,midg 2.3462020E-07 -2.8630371E-08 gauss-seidel spectral radius is 0.9903058 estimated iterations to convergence 83 setup time was (sec) 0.3600000 now iterating at: 08:33:18 rms-change max change #iterations 0.2425084 33.13737 at 10iterations 3.3133686E-02 3.899216 at 20iterations 4.5644352E-03 0.5851269 at 30iterations 7.8687875E-04 9.8438263E-02 at 40iterations 1.8971429E-04 2.6016235E-02 at 50iterations finished qdiffx linear iterations at : 08:33:21 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.8971429E-04 2.6016235E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 08:33:22 3.415u 0.182s 0:03.93 91.3% 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 08:33:22 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: SEP 177 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.200247 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): 41.26300 88.46301 ymin,ymax (A): -28.90400 13.25400 zmin,zma (A): -3.033000 45.50700 x,y,z range (A): 47.20001 42.15800 48.54000 scale (grids/A): 2.200247 object centre (A): 64.86300 -7.825000 21.23700 number of atom coordinates read : 2120 total number of charged atoms : 1988 net assigned charge : 5.564012 assigned positive charge : 325.3420 centred at (gu) : 87.40646 89.07893 91.62302 assigned negative charge : -319.7781 centred at (gu) : 87.80207 88.81397 91.38831 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 83440 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16867 grid for indexing accessible points = 1.400000 m= 34786 mr = 60940 m= 6976 mr = 27188 m= 693 mr = 4828 m= 34 mr = 398 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 378 time to turn everything in is 0.4200000 number of dielectric boundary points 32566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 15815 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) : 0.7334157 object centre at (A) : 64.86300 -7.825000 21.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1747490E-02 5.3251296E-02 midg,1,midg; midg,igrid,midg 2.7627949E-02 2.7181685E-02 1,midg,midg; igrid,midg,midg 4.7714725E-02 -5.6342646E-02 gauss-seidel spectral radius is 0.9989012 estimated iterations to convergence 239 setup time was (sec) 0.6400000 now iterating at: 08:33:23 rms-change max change #iterations 5.080478 207.2518 at 10iterations 2.564641 79.02426 at 20iterations 1.304181 38.18569 at 30iterations 0.6613094 19.50567 at 40iterations 0.3362050 9.264740 at 50iterations 0.1704341 4.912970 at 60iterations 8.6732820E-02 2.730110 at 70iterations 4.4171866E-02 1.179735 at 80iterations 2.2394195E-02 0.6033268 at 90iterations 1.1485241E-02 0.3355408 at 100iterations 5.9105880E-03 0.1601486 at 110iterations 3.1115571E-03 8.5237503E-02 at 120iterations finished qdiffx linear iterations at : 08:33:30 total time elapsed so far: 7.880000 # loops : 120 mean,max change (kT/e) : 3.1115571E-03 8.5237503E-02 energy calculations done at 7.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 08:33:30 8.017u 0.211s 0:08.84 92.9% 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 08:33:30 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2120 !!! WARNING: HIR 40 has a net charge of 0.5140 !!! WARNING: SEP 172 has a net charge of -0.4750 !!! WARNING: SEP 177 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.300371 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): 41.26300 88.46301 ymin,ymax (A): -28.90400 13.25400 zmin,zma (A): -3.033000 45.50700 x,y,z range (A): 47.20001 42.15800 48.54000 scale (grids/A): 3.300371 object centre (A): 64.86300 -7.825000 21.23700 number of atom coordinates read : 2120 total number of charged atoms : 1988 net assigned charge : 5.564012 assigned positive charge : 325.3420 centred at (gu) : 86.10963 88.61827 92.43448 assigned negative charge : -319.7781 centred at (gu) : 86.70313 88.22109 92.08244 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 192242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16867 grid for indexing accessible points = 1.400000 m= 107731 mr = 145832 m= 45091 mr = 91495 m= 13124 mr = 37892 m= 2681 mr = 10394 m= 394 mr = 1974 m= 25 mr = 284 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 1260 time to turn everything in is 1.300000 number of dielectric boundary points 73417 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 15904 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) : 2.200247 object centre at (A) : 64.86300 -7.825000 21.23700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1224931 0.4290259 midg,1,midg; midg,igrid,midg 0.2403564 0.1339771 1,midg,midg; igrid,midg,midg 0.4753673 -0.6800178 gauss-seidel spectral radius is 0.9993127 estimated iterations to convergence 301 setup time was (sec) 1.540000 now iterating at: 08:33:32 rms-change max change #iterations 10.95574 367.2154 at 10iterations 6.506736 121.2723 at 20iterations 3.851061 73.79334 at 30iterations 2.280315 45.13661 at 40iterations 1.348366 28.84699 at 50iterations 0.7951903 16.62092 at 60iterations 0.4692811 8.234547 at 70iterations 0.2765750 4.971754 at 80iterations 0.1631751 2.986992 at 90iterations 9.6136026E-02 1.677895 at 100iterations 5.6824446E-02 0.9881895 at 110iterations 3.3678483E-02 0.5167999 at 120iterations 2.0066502E-02 0.3569641 at 130iterations 1.2116451E-02 0.2099857 at 140iterations 7.4802609E-03 0.1386137 at 150iterations 4.8084655E-03 9.2983246E-02 at 160iterations 3.2634556E-03 5.5391312E-02 at 170iterations 2.3635733E-03 4.0830612E-02 at 180iterations finished qdiffx linear iterations at : 08:33:44 total time elapsed so far: 13.21000 # loops : 180 mean,max change (kT/e) : 2.3635733E-03 4.0830612E-02 energy calculations done at 13.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 08:33:45 13.333u 0.240s 0:14.14 95.9% 0+0k 0+0io 0pf+0w